Biological QA after resequencing of all the batches
Thomas Dobrenel and Nicolas Delhomme
2019-12-11
- 1 Setup
- 2 Raw data
- 3 Expression data
- 4 Data normalisation
- 5 Multivariate analysis
- 6 Differential expression based on all conditions compared to the T0
- 7 Comparisons of GOI lists (Venn diagrams)
- 8 Export list of DEGs
- 9 GO analysis
- 10 Session Info
1 Setup
- Set the working dir
setwd("/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/all-batches")- Load libraries
suppressPackageStartupMessages({
library(data.table)
library(DESeq2)
library(gplots)
library(here)
library(hyperSpec)
library(limma)
library(LSD)
library(magrittr)
library(matrixStats)
library(parallel)
library(pander)
library(plotly)
library(RColorBrewer)
library(scatterplot3d)
library(tidyverse)
library(tximport)
library(VennDiagram)
library(vsn)
})- Source some helper functions
suppressPackageStartupMessages({
source("~/Git/UPSCb/UPSCb-common/src/R/featureSelection.R")
source("~/Git/UPSCb/UPSCb-common/src/R/gopher.R")
source("~/Git/UPSCb/UPSCb-common/src/R/plot.multidensity.R")
source("~/Git/UPSCb/UPSCb-common/src/R/volcanoPlot.R")
})- Cutoff Different from Schurch et al., RNA, 2016 (LFC at 1 instead of 0,5)
lfc <- 1
FDR <- 0.01- Create palettes
pal <- c(brewer.pal(8,"Dark2"),1)
pal2 <- brewer.pal(9,"Paired") #require package RColorBrewer
cols <- rainbow(17)
hpal <- colorRampPalette(c("blue","white","red"))(100)- Register the default plot margin
mar <- par("mar")2 Raw data
2.1 Loading of sample information
- Read the sample information
samples <- read.csv("~/Git/UPSCb/projects/arabidopsis-nutrition-TOR/doc/samples3.csv")- Remove unnecessary samples
samples %<>% filter(!grepl("P11554_1",SciLifeID)) %>%
filter(! SciLifeID %in% c("P13406_101",
"P14066_128",
"P14066_133",
"P13406_102",
"P14066_131")) %>%
mutate(Nutrition,Nutrition=relevel(Nutrition,"NPS")) %>%
mutate(AZD,AZD=relevel(AZD,"DMSO"))
samples <- samples[order(samples$Timepoint, samples$Nutrition, samples$AZD),]
samples %<>% mutate(Timepoint,Timepoint=factor(paste0("T",Timepoint)))2.1.1 Load the data
- Call the data
filenames <- list.files("../Salmon",
recursive = TRUE,
pattern = "quant.sf",
full.names = TRUE)- Name the data
names(filenames) <- sub("_S.*","",sapply(strsplit(filenames, "/"), .subset, 3))- Match data <=> sample list
filenames <- filenames[match(samples$SciLifeID,names(filenames))]
filenames <-filenames[!is.na(names(filenames))]
samples <- samples[match(names(filenames),samples$SciLifeID),]- Annotate the samples
samples$Conditions <- factor(paste(samples$Timepoint,samples$Nutrition,samples$AZD,sep="_"))
samples$Batch <- factor(substr(samples$SciLifeID,1,8))3 Expression data
Read the expression at the transcript level
tx <- suppressMessages(tximport(files = filenames,
type = "salmon",
txOut = TRUE))summarise to genes
tx2gene <- data.frame(TXID=rownames(tx$counts),
GENEID=sub("\\.[0-9]+","",rownames(tx$counts)))
gx <- summarizeToGene(tx,tx2gene=tx2gene)## summarizing abundance## summarizing counts## summarizing lengthkg <- round(gx$counts) Sanity check
stopifnot(all(colnames(kg) == samples$SciLifeID))3.1 Raw data export
#dir.create(file.path("analysis_Tom","salmon"),showWarnings=FALSE,recursive=TRUE)
#write.table(kg,file="/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/nutrition-unormalised-gene-expression_data.csv")
#save(kg, samples, file = "/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/counts.rda")3.2 Preliminary validations
3.2.1 Check for the genes that are never expressed
sel <- rowSums(kg) == 0
sprintf("%s%% (%s) of %s genes are not expressed",
round(sum(sel) * 100/ nrow(kg),digits=1),
sum(sel),
nrow(kg))## [1] "16.9% (5452) of 32310 genes are not expressed"4 Data normalisation
For visualization, the data is submitted to a variance stabilization transformation using DESeq2. The dispersion is estimated independently of the sample type
dds <- DESeqDataSetFromMatrix(
countData = kg,
colData = samples,
design = ~ Conditions)## converting counts to integer modedds <- estimateSizeFactors(dds)4.1 Perform a Variance Stabilizing Transformation for plotting
vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)Write out
#write.csv(vst,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/library-size-normalized_variance-stabilized_data_nutrition.csv")5 Multivariate analysis
5.1 PCA
Principal Component Analysis on the normalized data * Establishment of the PCA
conditions1 <- factor(paste(samples$AZD,samples$Nutrition,sep="_"))
pc <- prcomp(t(vsd))
percent <- round(summary(pc)$importance[2,]*100);percent## PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16
## 46 21 14 6 3 2 1 1 1 0 0 0 0 0 0 0
## PC17 PC18 PC19 PC20 PC21 PC22 PC23 PC24 PC25 PC26 PC27 PC28 PC29 PC30 PC31 PC32
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## PC33 PC34 PC35 PC36 PC37 PC38 PC39 PC40 PC41 PC42 PC43 PC44 PC45 PC46 PC47 PC48
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## PC49 PC50 PC51 PC52 PC53 PC54 PC55 PC56
## 0 0 0 0 0 0 0 0- Graphical representation of PC1 x PC2
conds <- droplevels(conditions1)
plot(pc$x[,1],
pc$x[,2],
xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
ylab=paste("Comp. 2 (",percent[2],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("bottomright",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("topleft",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
- Graphical representation of PC2 x PC3
plot(pc$x[,2],
pc$x[,3],
xlab=paste("Comp. 2 (",percent[2],"%)",sep=""),
ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("topleft",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("bottomleft",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
- Graphical representation of PC1 x PC3
plot(pc$x[,1],
pc$x[,3],
xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("bottomleft",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("bottomright",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
6 Differential expression based on all conditions compared to the T0
6.1 Preparation of the design
sel <- samples$Timepoint %in% c("T0","T6","T24")
suppressMessages(dds <- DESeqDataSetFromMatrix(
countData = kg[,sel],
colData = samples[sel,],
design = ~ Conditions))6.2 Differential expression analysis
dds <- DESeq(dds)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 1 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing6.3 Variance Stabilising Transformation
6.3.1 Perform a Variance Stabilizing Transformation for plotting
vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)6.4 Contrasts to T0
The contrast by default is the first one (not Intercept)
resultsNames(dds)## [1] "Intercept" "Conditions_T24_NP_AZD_vs_T0_T0_0"
## [3] "Conditions_T24_NP_DMSO_vs_T0_T0_0" "Conditions_T24_NPS_AZD_vs_T0_T0_0"
## [5] "Conditions_T24_NPS_DMSO_vs_T0_T0_0" "Conditions_T24_NS_AZD_vs_T0_T0_0"
## [7] "Conditions_T24_NS_DMSO_vs_T0_T0_0" "Conditions_T24_PKS_AZD_vs_T0_T0_0"
## [9] "Conditions_T24_PKS_DMSO_vs_T0_T0_0" "Conditions_T6_NP_AZD_vs_T0_T0_0"
## [11] "Conditions_T6_NP_DMSO_vs_T0_T0_0" "Conditions_T6_NPS_AZD_vs_T0_T0_0"
## [13] "Conditions_T6_NPS_DMSO_vs_T0_T0_0" "Conditions_T6_NS_AZD_vs_T0_T0_0"
## [15] "Conditions_T6_NS_DMSO_vs_T0_T0_0" "Conditions_T6_PKS_AZD_vs_T0_T0_0"
## [17] "Conditions_T6_PKS_DMSO_vs_T0_T0_0"6.4.1 Different effects at T6
6.4.1.1 T6_NPS_DMSO
res <- results(dds,name = "Conditions_T6_NPS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NPSDMSO <- rownames(res[cutoffs,])
T6NPSDMSO_Low <- rownames(res[cutoff2,])
T6NPSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 5191 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 3163 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2028 genes that are repressed6.4.1.2 MA plot
DESeq2::plotMA(res)
6.4.1.3 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.4 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.5 T6_NPS_AZD
res <- results(dds,name = "Conditions_T6_NPS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NPSAZD <- rownames(res[cutoffs,])
T6NPSAZD_Low <- rownames(res[cutoff2,])
T6NPSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4567 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2624 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1943 genes that are repressed6.4.1.6 MA plot
DESeq2::plotMA(res)
6.4.1.7 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.8 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.9 T6_PKS_DMSO
res <- results(dds,name = "Conditions_T6_PKS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6PKSDMSO <- rownames(res[cutoffs,])
T6PKSDMSO_Low <- rownames(res[cutoff2,])
T6PKSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4647 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2905 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1742 genes that are repressed6.4.1.10 MA plot
DESeq2::plotMA(res)
6.4.1.11 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.12 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.13 T6_PKS_AZD
res <- results(dds,name = "Conditions_T6_PKS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6PKSAZD <- rownames(res[cutoffs,])
T6PKSAZD_Low <- rownames(res[cutoff2,])
T6PKSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4049 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2371 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1678 genes that are repressed6.4.1.14 MA plot
DESeq2::plotMA(res)
6.4.1.15 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.16 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.17 T6_NS_DMSO
res <- results(dds,name = "Conditions_T6_NS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NSDMSO <- rownames(res[cutoffs,])
T6NSDMSO_Low <- rownames(res[cutoff2,])
T6NSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 3375 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 1900 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1475 genes that are repressed6.4.1.18 MA plot
DESeq2::plotMA(res)
6.4.1.19 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.20 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.21 T6_NS_AZD
res <- results(dds,name = "Conditions_T6_NS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NSAZD <- rownames(res[cutoffs,])
T6NSAZD_Low <- rownames(res[cutoff2,])
T6NSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4801 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2686 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2115 genes that are repressed6.4.1.22 MA plot
DESeq2::plotMA(res)
6.4.1.23 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.24 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.25 T6_NP_DMSO
res <- results(dds,name = "Conditions_T6_NP_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NPDMSO <- rownames(res[cutoffs,])
T6NPDMSO_Low <- rownames(res[cutoff2,])
T6NPDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4952 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 3076 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1876 genes that are repressed6.4.1.26 MA plot
DESeq2::plotMA(res)
6.4.1.27 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.28 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.1.29 T6_NP_AZD
res <- results(dds,name = "Conditions_T6_NP_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T6NPAZD <- rownames(res[cutoffs,])
T6NPAZD_Low <- rownames(res[cutoff2,])
T6NPAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 3816 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2297 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1519 genes that are repressed6.4.1.30 MA plot
DESeq2::plotMA(res)
6.4.1.31 Volcano plot
volcanoPlot(res, lfc=1)
6.4.1.32 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2 Different effects at T24
6.4.2.1 T24_NPS_DMSO
res <- results(dds,name = "Conditions_T24_NPS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NPSDMSO <- rownames(res[cutoffs,])
T24NPSDMSO_Low <- rownames(res[cutoff2,])
T24NPSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 6290 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 3065 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 3225 genes that are repressed6.4.2.2 MA plot
DESeq2::plotMA(res)
6.4.2.3 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.4 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.5 T24_NPS_AZD
res <- results(dds,name = "Conditions_T24_NPS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NPSAZD <- rownames(res[cutoffs,])
T24NPSAZD_Low <- rownames(res[cutoff2,])
T24NPSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4410 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2128 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2282 genes that are repressed6.4.2.6 MA plot
DESeq2::plotMA(res)
6.4.2.7 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.8 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.9 T24_PKS_DMSO
res <- results(dds,name = "Conditions_T24_PKS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24PKSDMSO <- rownames(res[cutoffs,])
T24PKSDMSO_Low <- rownames(res[cutoff2,])
T24PKSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 5437 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2652 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2785 genes that are repressed6.4.2.10 MA plot
DESeq2::plotMA(res)
6.4.2.11 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.12 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.13 T24_PKS_AZD
res <- results(dds,name = "Conditions_T24_PKS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24PKSAZD <- rownames(res[cutoffs,])
T24PKSAZD_Low <- rownames(res[cutoff2,])
T24PKSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 3652 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 1750 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1902 genes that are repressed6.4.2.14 MA plot
DESeq2::plotMA(res)
6.4.2.15 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.16 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.17 T24_NS_DMSO
res <- results(dds,name = "Conditions_T24_NS_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NSDMSO <- rownames(res[cutoffs,])
T24NSDMSO_Low <- rownames(res[cutoff2,])
T24NSDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 1834 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 705 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 1129 genes that are repressed6.4.2.18 MA plot
DESeq2::plotMA(res)
6.4.2.19 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.20 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.21 T24_NS_AZD
res <- results(dds,name = "Conditions_T24_NS_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NSAZD <- rownames(res[cutoffs,])
T24NSAZD_Low <- rownames(res[cutoff2,])
T24NSAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 3499 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 1495 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2004 genes that are repressed6.4.2.22 MA plot
DESeq2::plotMA(res)
6.4.2.23 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.24 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.25 T24_NP_DMSO
res <- results(dds,name = "Conditions_T24_NP_DMSO_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NPDMSO <- rownames(res[cutoffs,])
T24NPDMSO_Low <- rownames(res[cutoff2,])
T24NPDMSO_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 5293 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2639 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2654 genes that are repressed6.4.2.26 MA plot
DESeq2::plotMA(res)
6.4.2.27 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.28 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
6.4.2.29 T24_NP_AZD
res <- results(dds,name = "Conditions_T24_NP_AZD_vs_T0_T0_0")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
T24NPAZD <- rownames(res[cutoffs,])
T24NPAZD_Low <- rownames(res[cutoff2,])
T24NPAZD_High <- rownames(res[cutoff1,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))## There are 4816 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1)))## There are 2539 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2)))## There are 2277 genes that are repressed6.4.2.30 MA plot
DESeq2::plotMA(res)
6.4.2.31 Volcano plot
volcanoPlot(res, lfc=1)
6.4.2.32 Heatmap
hm <- heatmap.2(t(scale(t(vsd[cutoffs,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
7 Comparisons of GOI lists (Venn diagrams)
7.1 GOI of nutrition at T6
- All GOI
grid.draw(venn.diagram(list(T6NPSDMSO, T6PKSDMSO, T6NSDMSO, T6NPDMSO),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
- Downregulated genes
grid.draw(venn.diagram(list(T6NPSDMSO_Low, T6PKSDMSO_Low, T6NSDMSO_Low, T6NPDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
- Upregulated genes
grid.draw(venn.diagram(list(T6NPSDMSO_High, T6PKSDMSO_High, T6NSDMSO_High, T6NPDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
7.2 GOI of AZD at T6
- All GOI
grid.draw(venn.diagram(list(T6NPSAZD, T6PKSAZD, T6NSAZD, T6NPAZD),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
- Downregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_Low, T6PKSAZD_Low, T6NSAZD_Low, T6NPAZD_Low),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
- Upregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_High, T6PKSAZD_High, T6NSAZD_High, T6NPAZD_High),
filename=NULL,
col=pal[1:4],
category.names=c("Full","No N","No P", "No C")))
7.3 Nutrition and AZD interaction at T6
7.3.1 For Carbon starvation
- Downregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_Low, T6NPSDMSO_Low, T6NPAZD_Low, T6NPDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Suc x AZD", "-Suc")))
- Upregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_High, T6NPSDMSO_High, T6NPAZD_High, T6NPDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Suc x AZD", "-Suc")))
7.3.2 For Phosphorus starvation
- Downregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_Low, T6NPSDMSO_Low, T6NSAZD_Low, T6NSDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Phos x AZD", "-Phos")))
- Upregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_High, T6NPSDMSO_High, T6NSAZD_High, T6NSDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Phos x AZD", "-Phos")))
7.3.3 For Nitrogen starvation
- Downregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_Low, T6NPSDMSO_Low, T6PKSAZD_Low, T6PKSDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Nit x AZD", "-Nit")))
- Upregulated genes
grid.draw(venn.diagram(list(T6NPSAZD_High, T6NPSDMSO_High, T6PKSAZD_High, T6PKSDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Nit x AZD", "-Nit")))
7.4 Nutrition and AZD interaction at T24
7.4.1 For Carbon starvation
- Downregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_Low, T24NPSDMSO_Low, T24NPAZD_Low, T24NPDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Suc x AZD", "-Suc")))
- Upregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_High, T24NPSDMSO_High, T24NPAZD_High, T24NPDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Suc x AZD", "-Suc")))
7.4.2 For Phosphorus starvation
- Downregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_Low, T24NPSDMSO_Low, T24NSAZD_Low, T24NSDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Phos x AZD", "-Phos")))
- Upregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_High, T24NPSDMSO_High, T24NSAZD_High, T24NSDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Phos x AZD", "-Phos")))
7.4.3 For Nitrogen starvation
- Downregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_Low, T24NPSDMSO_Low, T24PKSAZD_Low, T24PKSDMSO_Low),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Nit x AZD", "-Nit")))
- Upregulated genes
grid.draw(venn.diagram(list(T24NPSAZD_High, T24NPSDMSO_High, T24PKSAZD_High, T24PKSDMSO_High),
filename=NULL,
col=pal[1:4],
category.names=c("AZD","Ctrl","-Nit x AZD", "-Nit")))
8 Export list of DEGs
write.table(T6NPSDMSO_Low, file = "T6NPSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6PKSDMSO_Low, file = "T6PKSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NSDMSO_Low, file = "T6NSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NPDMSO_Low, file = "T6NPDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NPSDMSO_High, file = "T6NPSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T6PKSDMSO_High, file = "T6PKSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T6NSDMSO_High, file = "T6NSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T6NPDMSO_High, file = "T6NPDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T6NPSAZD_Low, file = "T6NPSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6PKSAZD_Low, file = "T6PKSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NSAZD_Low, file = "T6NSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NPAZD_Low, file = "T6NPAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T6NPSAZD_High, file = "T6NPSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T6PKSAZD_High, file = "T6PKSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T6NSAZD_High, file = "T6NSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T6NPAZD_High, file = "T6NPAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NPSDMSO_Low, file = "T24NPSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24PKSDMSO_Low, file = "T24PKSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NSDMSO_Low, file = "T24NSDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NPDMSO_Low, file = "T24NPDMSO_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NPSDMSO_High, file = "T24NPSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T24PKSDMSO_High, file = "T24PKSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NSDMSO_High, file = "T24NSDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NPDMSO_High, file = "T24NPDMSO_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NPSAZD_Low, file = "T24NPSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24PKSAZD_Low, file = "T24PKSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NSAZD_Low, file = "T24NSAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NPAZD_Low, file = "T24NPAZD_Low.txt", sep = "\t", row.names = FALSE)
write.table(T24NPSAZD_High, file = "T24NPSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T24PKSAZD_High, file = "T24PKSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NSAZD_High, file = "T24NSAZD_High.txt", sep = "\t", row.names = FALSE)
write.table(T24NPAZD_High, file = "T24NPAZD_High.txt", sep = "\t", row.names = FALSE)9 GO analysis
9.1 T6 DMSO
9.1.1 Induced genes
GO <- gopher(T6NPSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## Loading required package: jsonlite##
## Attaching package: 'jsonlite'## The following object is masked from 'package:purrr':
##
## flatten## No enrichments found in task: mapmanGO$go$name## [1] "ribonucleoprotein complex biogenesis"
## [2] "methylation"
## [3] "non-membrane-bounded organelle"
## [4] "cellular nitrogen compound metabolic process"
## [5] "thylakoid"
## [6] "RNA modification"
## [7] "structural molecule activity"
## [8] "ncRNA metabolic process"
## [9] "membrane-enclosed lumen"
## [10] "organelle"
## [11] "organic cyclic compound metabolic process"
## [12] "heterocycle metabolic process"
## [13] "ribonucleoprotein complex"
## [14] "cellular aromatic compound metabolic process"
## [15] "photosynthesis"
## [16] "DNA replication"
## [17] "protein-containing complex"
## [18] "pyrimidine-containing compound metabolic process"
## [19] "NADP metabolic process"
## [20] "plastid organization"
## [21] "metabolic process"
## [22] "intracellular"
## [23] "isoprenoid metabolic process"
## [24] "nuclear transport"
## [25] "cellular component organization or biogenesis"
## [26] "protein localization to nucleus"
## [27] "gene expression"
## [28] "organelle subcompartment"
## [29] "organophosphate metabolic process"
## [30] "rRNA metabolic process"
## [31] "response to red light"
## [32] "isopentenyl diphosphate metabolic process"
## [33] "peptide metabolic process"
## [34] "organelle organization"
## [35] "structural constituent of ribosome"
## [36] "protein alkylation"
## [37] "generation of precursor metabolites and energy"
## [38] "serine family amino acid metabolic process"
## [39] "plastid"
## [40] "RNA processing"
## [41] "plastid localization"
## [42] "heterocyclic compound binding"
## [43] "unsaturated fatty acid metabolic process"
## [44] "multicellular organism development"
## [45] "response to far red light"
## [46] "organic cyclic compound binding"
## [47] "ATPase activity"
## [48] "cellular process"
## [49] "response to blue light"
## [50] "response to abiotic stimulus"
## [51] "binding"
## [52] "apoplast"
## [53] "mitochondrion organization"
## [54] "carbohydrate derivative metabolic process"
## [55] "nitrogen compound metabolic process"
## [56] "mitochondrial transport"
## [57] "peptidyl-amino acid modification"
## [58] "macromolecule modification"
## [59] "nucleic acid transport"
## [60] "nucleoid"
## [61] "embryo sac development"
## [62] "plastid transcription"
## [63] "pyruvate metabolic process"
## [64] "oligosaccharide metabolic process"
## [65] "protein localization to mitochondrion"
## [66] "leaf development"
## [67] "post-embryonic plant morphogenesis"
## [68] "shoot system development"
## [69] "import into nucleus"
## [70] "nucleotidyltransferase activity"
## [71] "light-harvesting complex"
## [72] "regulation of metabolic process"
## [73] "response to oxygen-containing compound"
## [74] "RNA localization"
## [75] "establishment of localization in cell"
## [76] "catalytic activity, acting on DNA"
## [77] "glucose 6-phosphate metabolic process"
## [78] "PSII associated light-harvesting complex II catabolic process"
## [79] "tetrapyrrole binding"
## [80] "pigment metabolic process"
## [81] "biosynthetic process"
## [82] "protein-containing complex localization"
## [83] "cell population proliferation"
## [84] "ribonucleoprotein complex localization"
## [85] "phosphorus metabolic process"
## [86] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [87] "cellular biosynthetic process"
## [88] "multi-organism reproductive process"
## [89] "regulation of cell cycle"
## [90] "photosynthetic electron transport in photosystem I"
## [91] "response to red or far red light"
## [92] "transferase activity, transferring one-carbon groups"
## [93] "starch metabolic process"
## [94] "ER body"
## [95] "organonitrogen compound biosynthetic process"
## [96] "cellular response to DNA damage stimulus"
## [97] "cellular localization"
## [98] "photosystem"
## [99] "regulation of protein metabolic process"
## [100] "protein localization to organelle"
## [101] "glucan metabolic process"
## [102] "ribosome"
## [103] "membrane organization"
## [104] "response to acid chemical"
## [105] "oxidoreduction coenzyme metabolic process"
## [106] "DNA-dependent ATPase activity"
## [107] "regulation of reproductive process"
## [108] "establishment of organelle localization"
## [109] "plastoglobule"
## [110] "protein import"
## [111] "photosynthesis, light reaction"
## [112] "organophosphate biosynthetic process"
## [113] "tetraterpenoid metabolic process"
## [114] "mitochondrial RNA metabolic process"
## [115] "envelope"
## [116] "mitochondrion"
## [117] "cell cycle phase transition"
## [118] "multicellular organism reproduction"
## [119] "DNA conformation change"
## [120] "plant epidermis morphogenesis"
## [121] "macromolecule metabolic process"
## [122] "nitrogen compound transport"
## [123] "DNA polymerase complex"
## [124] "response to stress"
## [125] "response to cytokinin"
## [126] "homeostatic process"
## [127] "regulation of neurotransmitter levels"
## [128] "positive regulation of molecular function"
## [129] "hydrolase activity, acting on acid anhydrides"
## [130] "carbon fixation"
## [131] "stomatal complex development"
## [132] "long-day photoperiodism"
## [133] "shoot system morphogenesis"
## [134] "gene silencing"
## [135] "plastid stroma"
## [136] "cellular response to environmental stimulus"
## [137] "ligase activity, forming nitrogen-metal bonds"
## [138] "phosphatidylglycerol metabolic process"
## [139] "regulation of DNA recombination"
## [140] "spindle organization"
## [141] "organic substance metabolic process"
## [142] "regulation of molecular function"
## [143] "single-stranded RNA binding"GO$kegg$id## [1] "3.6.4.13" "1.97.1.12" "1.10.3.9" "1.18.1.2" "2.7.7.6"GO$pfam$name## [1] "PPR repeat family"
## [2] "PPR repeat"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Pentatricopeptide repeat domain"
## [5] "Core histone H2A/H2B/H3/H4"
## [6] "PPR repeat"
## [7] "Chlorophyll A-B binding protein"
## [8] "mTERF"
## [9] "Brix domain"
## [10] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [11] "Plant organelle RNA recognition domain"
## [12] "C-terminus of histone H2A"
## [13] "MCM N-terminal domain"
## [14] "MCM P-loop domain"
## [15] "Helicase conserved C-terminal domain"
## [16] "Dip2/Utp12 Family"
## [17] "PsbP"
## [18] "Ribosomal protein S5, C-terminal domain"
## [19] "Ribosomal protein S5, N-terminal domain"
## [20] "60s Acidic ribosomal protein"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NPSDMSO_High <- GO
GO <- gopher(T6NSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "thylakoid"
## [2] "photosynthesis"
## [3] "plastid organization"
## [4] "organelle subcompartment"
## [5] "secondary metabolic process"
## [6] "response to stimulus"
## [7] "generation of precursor metabolites and energy"
## [8] "ion transport"
## [9] "light-harvesting complex"
## [10] "protein localization to membrane"
## [11] "glucose 6-phosphate metabolic process"
## [12] "response to acid chemical"
## [13] "response to oxygen-containing compound"
## [14] "response to red light"
## [15] "tetrapyrrole binding"
## [16] "NADP metabolic process"
## [17] "pigment metabolic process"
## [18] "oxygen binding"
## [19] "tetrapyrrole metabolic process"
## [20] "flavonoid metabolic process"
## [21] "response to endogenous stimulus"
## [22] "response to far red light"
## [23] "protein-containing complex subunit organization"
## [24] "sulfur compound metabolic process"
## [25] "glycosyl compound metabolic process"
## [26] "drug metabolic process"
## [27] "plastid"
## [28] "regulation of protein metabolic process"
## [29] "small molecule biosynthetic process"
## [30] "response to chemical"
## [31] "serine family amino acid metabolic process"
## [32] "ribonucleoprotein complex biogenesis"
## [33] "PSII associated light-harvesting complex II catabolic process"
## [34] "rhythmic process"
## [35] "biological regulation"
## [36] "cell death"
## [37] "cellular response to environmental stimulus"
## [38] "oxidoreductase activity"
## [39] "dephosphorylation"
## [40] "extracellular region"
## [41] "starch metabolic process"
## [42] "single-stranded RNA binding"
## [43] "DNA binding"
## [44] "oxidation-reduction process"
## [45] "cofactor binding"
## [46] "reactive oxygen species metabolic process"
## [47] "response to blue light"
## [48] "aging"
## [49] "immune system process"
## [50] "indole-containing compound metabolic process"
## [51] "ncRNA metabolic process"
## [52] "small molecule metabolic process"
## [53] "RNA metabolic process"
## [54] "chemical homeostasis"
## [55] "response to inorganic substance"
## [56] "plastid envelope"
## [57] "sulfur compound biosynthetic process"
## [58] "cofactor metabolic process"
## [59] "oligosaccharide metabolic process"
## [60] "response to light stimulus"
## [61] "unsaturated fatty acid metabolic process"
## [62] "plastid stroma"
## [63] "organic acid metabolic process"
## [64] "cellular homeostasis"
## [65] "de-etiolation"
## [66] "response to disaccharide"
## [67] "organic hydroxy compound metabolic process"
## [68] "ER body"
## [69] "response to abiotic stimulus"
## [70] "regulation of seedling development"
## [71] "rRNA metabolic process"
## [72] "peptidyl-cysteine modification"
## [73] "membrane-bounded organelle"
## [74] "leaf development"
## [75] "benzene-containing compound metabolic process"
## [76] "multi-organism process"
## [77] "cell communication"
## [78] "response to biotic stimulus"
## [79] "multi-organism cellular process"
## [80] "protein targeting"
## [81] "inorganic ion transmembrane transport"
## [82] "intramolecular lyase activity"
## [83] "plastoglobule"
## [84] "cellular component disassembly"
## [85] "apoplast"
## [86] "organic hydroxy compound biosynthetic process"
## [87] "membrane"
## [88] "response to stress"
## [89] "oxidoreduction coenzyme metabolic process"
## [90] "response to osmotic stress"
## [91] "response to wounding"
## [92] "response to lipid"
## [93] "positive regulation of molecular function"
## [94] "aromatic compound biosynthetic process"
## [95] "lipid metabolic process"
## [96] "amine metabolic process"
## [97] "localization"
## [98] "shoot system morphogenesis"
## [99] "photosynthetic electron transport in photosystem I"
## [100] "regulation of response to stimulus"
## [101] "secondary active transmembrane transporter activity"
## [102] "establishment of localization in cell"
## [103] "protein domain specific binding"
## [104] "photosynthetic membrane"
## [105] "protein repair"
## [106] "regulation of biological quality"
## [107] "auxin metabolic process"
## [108] "transcription regulator activity"
## [109] "axis specification"
## [110] "long-day photoperiodism"
## [111] "envelope"
## [112] "photosynthesis, light reaction"
## [113] "transferase activity, transferring alkyl or aryl (other than methyl) groups"GO$kegg$id## [1] "1.10.3.9" "1.18.1.2" "3.1.1.1" "1.97.1.12" "1.14.13.173"
## [6] "2.4.2.51" "1.2.1.13" "3.2.1.21" "2.8.2.24" "2.4.1.263"GO$pfam$name## [1] "Chlorophyll A-B binding protein"
## [2] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [3] "Cytochrome P450"
## [4] "Dehydrin"
## [5] "Carboxylesterase family"
## [6] "Leucine Rich Repeat"
## [7] "CP12 domain"
## [8] "Hsp20/alpha crystallin family"
## [9] "Cysteine-rich TM module stress tolerance"
## [10] "No apical meristem (NAM) protein"
## [11] "zinc-finger of the FCS-type, C2-C2"
## [12] "Oxidoreductase NAD-binding domain"
## [13] "non-haem dioxygenase in morphine synthesis N-terminal"
## [14] "Glycosyl hydrolase family 1"
## [15] "Putative nuclear localisation signal"
## [16] "Late embryogenesis abundant (LEA) group 1"
## [17] "NAF domain"
## [18] "MatE"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NSDMSO_High <- GO
GO <- gopher(T6PKSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "ribonucleoprotein complex biogenesis"
## [2] "methylation"
## [3] "non-membrane-bounded organelle"
## [4] "structural molecule activity"
## [5] "cellular nitrogen compound metabolic process"
## [6] "membrane-enclosed lumen"
## [7] "RNA modification"
## [8] "protein-containing complex"
## [9] "ncRNA metabolic process"
## [10] "ribonucleoprotein complex"
## [11] "DNA replication"
## [12] "organelle"
## [13] "thylakoid"
## [14] "organic cyclic compound metabolic process"
## [15] "heterocycle metabolic process"
## [16] "pyrimidine-containing compound metabolic process"
## [17] "cellular aromatic compound metabolic process"
## [18] "protein alkylation"
## [19] "nuclear transport"
## [20] "cellular component organization or biogenesis"
## [21] "protein localization to nucleus"
## [22] "structural constituent of ribosome"
## [23] "metabolic process"
## [24] "photosynthesis"
## [25] "intracellular"
## [26] "gene expression"
## [27] "peptidyl-amino acid modification"
## [28] "organelle organization"
## [29] "heterocyclic compound binding"
## [30] "NADP metabolic process"
## [31] "peptide metabolic process"
## [32] "organic cyclic compound binding"
## [33] "RNA processing"
## [34] "organophosphate metabolic process"
## [35] "nitrogen compound metabolic process"
## [36] "mitochondrial transport"
## [37] "isoprenoid metabolic process"
## [38] "rRNA metabolic process"
## [39] "cellular process"
## [40] "macromolecule modification"
## [41] "isopentenyl diphosphate metabolic process"
## [42] "nucleotidyltransferase activity"
## [43] "mitochondrion organization"
## [44] "apoplast"
## [45] "ATPase activity"
## [46] "embryo sac development"
## [47] "transferase activity, transferring one-carbon groups"
## [48] "cell population proliferation"
## [49] "plastid organization"
## [50] "response to red light"
## [51] "ribosome"
## [52] "nitrogen compound transport"
## [53] "organelle subcompartment"
## [54] "multi-organism reproductive process"
## [55] "post-embryonic plant morphogenesis"
## [56] "RNA localization"
## [57] "cytosol"
## [58] "catalytic activity, acting on DNA"
## [59] "protein localization to mitochondrion"
## [60] "multicellular organism development"
## [61] "light-harvesting complex"
## [62] "ribonucleoprotein complex localization"
## [63] "unsaturated fatty acid metabolic process"
## [64] "import into nucleus"
## [65] "protein-containing complex localization"
## [66] "response to blue light"
## [67] "organonitrogen compound biosynthetic process"
## [68] "serine family amino acid metabolic process"
## [69] "cellular localization"
## [70] "regulation of reproductive process"
## [71] "gene silencing"
## [72] "cellular amide metabolic process"
## [73] "plastid localization"
## [74] "response to far red light"
## [75] "mitochondrion"
## [76] "leaf development"
## [77] "tetrapyrrole binding"
## [78] "DNA-dependent ATPase activity"
## [79] "protein localization to organelle"
## [80] "catalytic activity, acting on RNA"
## [81] "carbohydrate derivative metabolic process"
## [82] "organic substance transport"
## [83] "cellular response to DNA damage stimulus"
## [84] "cellular biosynthetic process"
## [85] "protein import"
## [86] "nucleoid"
## [87] "gametophyte development"
## [88] "photosynthesis, light reaction"
## [89] "ER body"
## [90] "positive regulation of chromosome organization"
## [91] "nuclease activity"
## [92] "macromolecule metabolic process"
## [93] "plastid transcription"
## [94] "nucleobase-containing small molecule metabolic process"
## [95] "regulation of cell cycle"
## [96] "biosynthetic process"
## [97] "shoot system development"
## [98] "multicellular organism reproduction"
## [99] "RNA phosphodiester bond hydrolysis"
## [100] "response to oxygen-containing compound"
## [101] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [102] "nucleic acid transport"
## [103] "corolla development"
## [104] "cellular process involved in reproduction in multicellular organism"
## [105] "cell cycle phase transition"
## [106] "phosphorus metabolic process"
## [107] "hydrolase activity, acting on acid anhydrides"
## [108] "flower calyx development"
## [109] "transition metal ion binding"
## [110] "response to abiotic stimulus"
## [111] "organophosphate biosynthetic process"
## [112] "macromolecule localization"
## [113] "plastid stroma"
## [114] "generation of precursor metabolites and energy"
## [115] "photosynthetic electron transport in photosystem I"
## [116] "carbon fixation"
## [117] "starch metabolic process"
## [118] "amidophosphoribosyltransferase activity"
## [119] "DNA metabolic process"
## [120] "plastid"
## [121] "organic substance metabolic process"
## [122] "phosphatidylglycerol metabolic process"
## [123] "PSII associated light-harvesting complex II catabolic process"
## [124] "negative regulation of gene expression, epigenetic"
## [125] "response to cytokinin"
## [126] "single-stranded RNA binding"
## [127] "DNA polymerase complex"
## [128] "NADPH dehydrogenase activity"
## [129] "homeostatic process"
## [130] "DNA conformation change"
## [131] "mitochondrial RNA metabolic process"
## [132] "plant organ formation"GO$kegg$id## [1] "3.6.4.13" "1.97.1.12" "2.7.7.6" "1.10.3.9" "2.4.2.14" "1.2.1.13"
## [7] "2.1.1.125" "2.4.2.51"GO$pfam$name## [1] "PPR repeat family"
## [2] "PPR repeat"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Core histone H2A/H2B/H3/H4"
## [5] "Chlorophyll A-B binding protein"
## [6] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [7] "Pentatricopeptide repeat domain"
## [8] "60s Acidic ribosomal protein"
## [9] "C-terminus of histone H2A"
## [10] "Brix domain"
## [11] "PPR repeat"
## [12] "Helicase conserved C-terminal domain"
## [13] "mTERF"
## [14] "MCM N-terminal domain"
## [15] "DEAD/DEAH box helicase"
## [16] "MCM P-loop domain"
## [17] "Plant organelle RNA recognition domain"
## [18] "Dip2/Utp12 Family"
## [19] "Ribosomal protein S5, C-terminal domain"
## [20] "Ribosomal protein S5, N-terminal domain"
## [21] "Dimerisation domain"
## [22] "NOP5NT (NUC127) domain"
## [23] "DNA polymerase family B, exonuclease domain"
## [24] "DNA polymerase family B"
## [25] "MutS domain I"
## [26] "Replication factor-A C terminal domain"
## [27] "Replication factor-A protein 1, N-terminal domain"
## [28] "Replication protein A OB domain"
## [29] "Ribosomal protein L1p/L10e family"
## [30] "O-methyltransferase domain"
## [31] "CBF/Mak21 family"
## [32] "RS4NT (NUC023) domain"
## [33] "Ribosomal protein L37e"
## [34] "BRCA1 C Terminus (BRCT) domain"
## [35] "Rad9"
## [36] "Gar1/Naf1 RNA binding region"
## [37] "40S ribosomal protein S4 C-terminus"
## [38] "Ribosomal L27e protein family"
## [39] "Single-strand binding protein family"
## [40] "Ribosomal family S4e"
## [41] "DNA-dependent RNA polymerase"
## [42] "DNA-directed RNA polymerase N-terminal"
## [43] "Ribosomal L28e protein family"
## [44] "Ribosomal L22e protein family"
## [45] "Tetrapyrrole (Corrin/Porphyrin) Methylases"
## [46] "Protein of unknown function (DUF627)"
## [47] "Protein of unknown function (DUF629)"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6PKSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T6PKSDMSO_High <- GO
GO <- gopher(T6NPDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "non-membrane-bounded organelle"
## [2] "ribonucleoprotein complex biogenesis"
## [3] "methylation"
## [4] "structural molecule activity"
## [5] "cellular nitrogen compound metabolic process"
## [6] "ribonucleoprotein complex"
## [7] "protein-containing complex"
## [8] "membrane-enclosed lumen"
## [9] "organelle"
## [10] "heterocycle metabolic process"
## [11] "RNA modification"
## [12] "organic cyclic compound metabolic process"
## [13] "cellular aromatic compound metabolic process"
## [14] "pyrimidine-containing compound metabolic process"
## [15] "ncRNA metabolic process"
## [16] "DNA replication"
## [17] "intracellular"
## [18] "gene expression"
## [19] "nitrogen compound metabolic process"
## [20] "structural constituent of ribosome"
## [21] "nuclear transport"
## [22] "protein alkylation"
## [23] "cellular component organization or biogenesis"
## [24] "metabolic process"
## [25] "thylakoid"
## [26] "peptide metabolic process"
## [27] "organelle organization"
## [28] "protein localization to nucleus"
## [29] "mitochondrial transport"
## [30] "protein localization to organelle"
## [31] "ribosome"
## [32] "macromolecule metabolic process"
## [33] "heterocyclic compound binding"
## [34] "cellular process"
## [35] "peptidyl-amino acid modification"
## [36] "organic cyclic compound binding"
## [37] "isoprenoid metabolic process"
## [38] "organophosphate metabolic process"
## [39] "nucleotidyltransferase activity"
## [40] "photosynthesis"
## [41] "mitochondrion organization"
## [42] "cellular amide metabolic process"
## [43] "multi-organism reproductive process"
## [44] "cytosol"
## [45] "embryo sac development"
## [46] "RNA localization"
## [47] "mitochondrion"
## [48] "cellular response to DNA damage stimulus"
## [49] "protein-containing complex localization"
## [50] "ribonucleoprotein complex localization"
## [51] "cell population proliferation"
## [52] "RNA processing"
## [53] "catalytic activity, acting on RNA"
## [54] "nuclease activity"
## [55] "NADP metabolic process"
## [56] "nucleoid"
## [57] "serine family amino acid metabolic process"
## [58] "isopentenyl diphosphate metabolic process"
## [59] "protein localization to mitochondrion"
## [60] "cellular biosynthetic process"
## [61] "organonitrogen compound biosynthetic process"
## [62] "protein import"
## [63] "multicellular organism reproduction"
## [64] "rRNA metabolic process"
## [65] "post-embryonic plant morphogenesis"
## [66] "multicellular organism development"
## [67] "catalytic activity, acting on DNA"
## [68] "macromolecule modification"
## [69] "gametophyte development"
## [70] "biosynthetic process"
## [71] "transferase activity, transferring one-carbon groups"
## [72] "import into nucleus"
## [73] "cellular localization"
## [74] "gene silencing"
## [75] "organic substance metabolic process"
## [76] "cellular process involved in reproduction in multicellular organism"
## [77] "unsaturated fatty acid metabolic process"
## [78] "plastid organization"
## [79] "nucleic acid transport"
## [80] "binding"
## [81] "ATPase activity"
## [82] "response to cytokinin"
## [83] "plastid localization"
## [84] "response to red light"
## [85] "apoplast"
## [86] "plastid transcription"
## [87] "cellular metabolic process"
## [88] "shoot system development"
## [89] "DNA-dependent ATPase activity"
## [90] "organophosphate biosynthetic process"
## [91] "plastid stroma"
## [92] "external encapsulating structure"
## [93] "nitrogen compound transport"
## [94] "response to red or far red light"
## [95] "regulation of metabolic process"
## [96] "response to blue light"
## [97] "nucleobase-containing compound transport"
## [98] "light-harvesting complex"
## [99] "response to abiotic stimulus"
## [100] "nucleobase-containing compound metabolic process"
## [101] "nucleobase-containing small molecule metabolic process"
## [102] "ER body"
## [103] "negative regulation of gene expression, epigenetic"
## [104] "tetrapyrrole binding"
## [105] "pyruvate metabolic process"
## [106] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [107] "organelle subcompartment"
## [108] "carbohydrate derivative metabolic process"
## [109] "regulation of reproductive process"
## [110] "macromolecule localization"
## [111] "regulation of cell cycle"
## [112] "hydrolase activity, acting on acid anhydrides"
## [113] "DNA metabolic process"
## [114] "primary metabolic process"
## [115] "cell cycle phase transition"
## [116] "homeostatic process"
## [117] "cell differentiation"
## [118] "chromosome segregation"
## [119] "photosynthetic electron transport in photosystem I"
## [120] "response to far red light"
## [121] "organic substance transport"
## [122] "response to ionizing radiation"
## [123] "mitochondrial RNA metabolic process"
## [124] "response to carbohydrate"
## [125] "protein modification by small protein conjugation"
## [126] "plant organ formation"
## [127] "leaf development"
## [128] "RNA phosphodiester bond hydrolysis"
## [129] "plastid"
## [130] "flower calyx development"
## [131] "phosphatidylglycerol metabolic process"
## [132] "chromosome organization"
## [133] "protein acetylation"
## [134] "histone H3-K9 modification"
## [135] "positive regulation of chromosome organization"
## [136] "oxidoreduction coenzyme metabolic process"
## [137] "amide transport"
## [138] "long-day photoperiodism"
## [139] "glucan metabolic process"
## [140] "establishment of organelle localization"
## [141] "amidophosphoribosyltransferase activity"
## [142] "corolla development"
## [143] "ligase activity"
## [144] "pseudouridine synthase activity"GO$kegg$id## [1] "3.6.4.13" "2.7.7.6" "1.97.1.12" "1.10.3.9" "3.6.4.12" "3.1.26.5"
## [7] "2.4.2.14" "1.2.1.13" "2.1.1.125" "2.4.2.51"GO$pfam$name## [1] "PPR repeat family"
## [2] "PPR repeat"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Pentatricopeptide repeat domain"
## [5] "Core histone H2A/H2B/H3/H4"
## [6] "PPR repeat"
## [7] "60s Acidic ribosomal protein"
## [8] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [9] "mTERF"
## [10] "Chlorophyll A-B binding protein"
## [11] "C-terminus of histone H2A"
## [12] "Plant organelle RNA recognition domain"
## [13] "Brix domain"
## [14] "Helicase conserved C-terminal domain"
## [15] "MCM N-terminal domain"
## [16] "MCM P-loop domain"
## [17] "DEAD/DEAH box helicase"
## [18] "Ribosomal protein L3"
## [19] "Dip2/Utp12 Family"
## [20] "Ribosomal protein L21e"
## [21] "KOW motif"
## [22] "Ribosomal protein S5, C-terminal domain"
## [23] "Protein of unknown function (DUF627)"
## [24] "Domain of unknown function (DUF3444)"
## [25] "Protein of unknown function (DUF629)"
## [26] "3 exoribonuclease family, domain 1"
## [27] "Ribosomal protein S5, N-terminal domain"
## [28] "E2F/DP family winged-helix DNA-binding domain"
## [29] "MutS domain I"
## [30] "Ribosomal protein L5"
## [31] "DNA polymerase family B"
## [32] "NOP5NT (NUC127) domain"
## [33] "DNA polymerase family B, exonuclease domain"
## [34] "von Willebrand factor type A domain"
## [35] "ribosomal L5P family C-terminus"
## [36] "Centromere kinetochore component CENP-T histone fold"
## [37] "3 exoribonuclease family, domain 2"
## [38] "Replication factor-A C terminal domain"
## [39] "Replication protein A OB domain"
## [40] "Replication factor-A protein 1, N-terminal domain"
## [41] "Ribosomal protein L1p/L10e family"
## [42] "F-box domain"
## [43] "Ribosomal L28e protein family"
## [44] "Plectin/S10 domain"
## [45] "RS4NT (NUC023) domain"
## [46] "Ribosomal protein L37e"
## [47] "BRCA1 C Terminus (BRCT) domain"
## [48] "Rad9"
## [49] "Ribosomal L22e protein family"
## [50] "CBF/Mak21 family"
## [51] "40S ribosomal protein S4 C-terminus"
## [52] "Ribosomal family S4e"
## [53] "S1 RNA binding domain"
## [54] "Ribosomal protein S19e"
## [55] "Ribosomal L27e protein family"
## [56] "Ribosomal_S17 N-terminal"
## [57] "Gar1/Naf1 RNA binding region"
## [58] "Leucine Rich Repeat"
## [59] "OST-HTH Associated domain"
## [60] "Single-strand binding protein family"
## [61] "Ribosomal protein L24e"
## [62] "Ribosomal protein S8e"
## [63] "Ribosomal protein L36e"
## [64] "DNA-dependent RNA polymerase"
## [65] "DNA-directed RNA polymerase N-terminal"
## [66] "RING-like zinc finger"
## [67] "Nucleosome assembly protein (NAP)"
## [68] "SAM domain (Sterile alpha motif)"
## [69] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [70] "Ribosomal protein L13"
## [71] "Ribosomal Proteins L2, C-terminal domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NPDMSO_High <- GO9.1.2 Repressed genes
GO <- gopher(T6NPSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "liposaccharide metabolic process"
## [3] "cell communication"
## [4] "response to stimulus"
## [5] "membrane lipid metabolic process"
## [6] "membrane"
## [7] "extracellular region"
## [8] "response to drug"
## [9] "endomembrane system"
## [10] "response to light intensity"
## [11] "cellular response to phosphate starvation"
## [12] "lipid metabolic process"
## [13] "response to nitrogen compound"
## [14] "cellular response to external stimulus"
## [15] "symplast"
## [16] "cell junction"
## [17] "response to heat"
## [18] "response to extracellular stimulus"
## [19] "protein folding"
## [20] "regulation of biological quality"
## [21] "response to oxygen-containing compound"
## [22] "carbohydrate metabolic process"
## [23] "organic hydroxy compound metabolic process"
## [24] "cytoskeleton"
## [25] "external encapsulating structure organization"
## [26] "cell wall organization or biogenesis"
## [27] "root system development"
## [28] "response to oxidative stress"
## [29] "response to external stimulus"
## [30] "root hair cell development"
## [31] "protein localization to membrane"
## [32] "cell development"
## [33] "growth"
## [34] "cellular response to stimulus"
## [35] "plant epidermal cell differentiation"
## [36] "response to antibiotic"
## [37] "structural constituent of cell wall"
## [38] "respiratory burst"
## [39] "regulation of meristem development"
## [40] "signaling"
## [41] "immune system process"
## [42] "phosphate ion transport"
## [43] "drug metabolic process"
## [44] "external encapsulating structure"
## [45] "protein polymerization"
## [46] "vacuole"
## [47] "benzene-containing compound metabolic process"
## [48] "cytoskeleton organization"
## [49] "cellular modified amino acid biosynthetic process"
## [50] "response to wounding"
## [51] "anchored component of membrane"
## [52] "phosphate ion transmembrane transporter activity"
## [53] "polysaccharide localization"
## [54] "amine metabolic process"
## [55] "phosphorylation"
## [56] "response to unfolded protein"
## [57] "guanyl nucleotide binding"
## [58] "response to endoplasmic reticulum stress"
## [59] "nucleoside binding"
## [60] "regulation of cell size"
## [61] "acid phosphatase activity"
## [62] "hydrolase activity, acting on glycosyl bonds"
## [63] "response to monosaccharide"
## [64] "transferase activity, transferring glycosyl groups"
## [65] "catalytic activity"
## [66] "cell death"
## [67] "localization"
## [68] "pigmentation"
## [69] "indole-containing compound metabolic process"
## [70] "protein localization to vacuole"
## [71] "phosphoric ester hydrolase activity"
## [72] "transporter activity"
## [73] "carbohydrate derivative biosynthetic process"
## [74] "inorganic phosphate transmembrane transporter activity"
## [75] "purine-containing compound metabolic process"
## [76] "vesicle"
## [77] "regulation of hormone levels"
## [78] "carbohydrate derivative metabolic process"
## [79] "meristem maintenance"
## [80] "response to mechanical stimulus"
## [81] "multidimensional cell growth"
## [82] "hydrolase activity, acting on ester bonds"
## [83] "response to light stimulus"
## [84] "UDP-glucose 6-dehydrogenase activity"
## [85] "response to chemical"
## [86] "DNA binding"
## [87] "response to nutrient levels"
## [88] "cell plate"
## [89] "cellular macromolecule metabolic process"
## [90] "tissue development"
## [91] "energy derivation by oxidation of organic compounds"
## [92] "structural constituent of cytoskeleton"
## [93] "syncytium formation"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.4.23.12" "3.2.1.151" "3.1.4.46" "3.6.1.1"
## [7] "1.10.3.3" "2.4.1.46" "1.11.1.9"GO$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "Glycerophosphoryl diester phosphodiesterase family"
## [4] "Purple acid Phosphatase, N-terminal domain"
## [5] "Iron/zinc purple acid phosphatase-like protein C"
## [6] "ADP-ribosylation factor family"
## [7] "Eukaryotic aspartyl protease"
## [8] "Arabinogalactan peptide"
## [9] "Fasciclin domain"
## [10] "Major Facilitator Superfamily"
## [11] "Calcineurin-like phosphoesterase"
## [12] "Calreticulin family"
## [13] "Protein of unknown function (DUF1005)"
## [14] "Domain of unknown function (DUF4228)"
## [15] "C2H2-type zinc finger"
## [16] "Hsp70 protein"
## [17] "Xylanase inhibitor N-terminal"
## [18] "Glycosyl hydrolase family 9"
## [19] "Hsp20/alpha crystallin family"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NPSDMSO_Low <- GO
GO <- gopher(T6NSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "microtubule-based process"
## [3] "extracellular region"
## [4] "cytoskeleton organization"
## [5] "steroid metabolic process"
## [6] "response to heat"
## [7] "growth"
## [8] "cell junction"
## [9] "cell division"
## [10] "symplast"
## [11] "protein folding"
## [12] "membrane"
## [13] "cell wall organization or biogenesis"
## [14] "motor activity"
## [15] "intrinsic component of membrane"
## [16] "nucleoside bisphosphate metabolic process"
## [17] "response to light intensity"
## [18] "cytoskeleton"
## [19] "anchored component of membrane"
## [20] "hydrolase activity, acting on glycosyl bonds"
## [21] "external encapsulating structure"
## [22] "response to mechanical stimulus"
## [23] "response to oxidative stress"
## [24] "flower calyx development"
## [25] "response to endoplasmic reticulum stress"
## [26] "structural constituent of cytoskeleton"
## [27] "DNA replication"
## [28] "external encapsulating structure organization"
## [29] "phosphorylation"
## [30] "signaling"
## [31] "protein polymerization"
## [32] "cell cycle"
## [33] "cell population proliferation"
## [34] "response to wounding"
## [35] "cell cycle phase transition"
## [36] "response to drug"
## [37] "cytokinesis"
## [38] "cell communication"
## [39] "biological regulation"
## [40] "response to brassinosteroid"
## [41] "corolla development"
## [42] "tubulin complex"
## [43] "thioester metabolic process"
## [44] "regulation of meristem development"
## [45] "cellular modified amino acid biosynthetic process"
## [46] "negative regulation of gene expression, epigenetic"
## [47] "plant-type cell wall"
## [48] "oligopeptide transport"
## [49] "protein localization to membrane"
## [50] "mitotic cell cycle process"
## [51] "response to nitrogen compound"
## [52] "carbon-oxygen lyase activity, acting on polysaccharides"
## [53] "calmodulin binding"
## [54] "response to stimulus"
## [55] "response to chemical"
## [56] "organelle assembly"
## [57] "organic hydroxy compound metabolic process"
## [58] "coenzyme metabolic process"
## [59] "shade avoidance"
## [60] "DNA binding"
## [61] "vacuole"
## [62] "endomembrane system"
## [63] "galacturonan metabolic process"
## [64] "cellular macromolecule metabolic process"
## [65] "respiratory burst"
## [66] "pigmentation"
## [67] "response to cyclopentenone"
## [68] "structural constituent of cell wall"
## [69] "multidimensional cell growth"
## [70] "protein alkylation"
## [71] "regulation of mitotic cell cycle"
## [72] "cell development"
## [73] "root hair cell development"
## [74] "tissue development"
## [75] "DNA modification"
## [76] "alpha-amino acid metabolic process"
## [77] "cellular response to stimulus"
## [78] "kinase activity"
## [79] "hydrolase activity"
## [80] "carbon-oxygen lyase activity"
## [81] "post-embryonic plant organ development"
## [82] "xyloglucan:xyloglucosyl transferase activity"
## [83] "mitotic checkpoint complex"
## [84] "meristem maintenance"
## [85] "response to oxygen-containing compound"
## [86] "regulation of cell cycle"
## [87] "anatomical structure formation involved in morphogenesis"
## [88] "phosphotransferase activity, alcohol group as acceptor"
## [89] "ribose phosphate metabolic process"
## [90] "indole-containing compound metabolic process"
## [91] "regulation of hormone levels"GO$kegg$id## [1] "2.4.1.207" "3.6.4.4" "1.10.3.3" "4.2.2.2" "3.4.23.12"
## [6] "3.2.1.4" "3.6.4.5" "3.2.1.151" "1.11.1.7" "2.7.11.1"
## [11] "3.2.1.39" "3.1.1.11" "1.14.13.93"GO$pfam$name## [1] "Kinesin motor domain"
## [2] "Leucine rich repeat N-terminal domain"
## [3] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [4] "Glycosyl hydrolases family 16"
## [5] "Fasciclin domain"
## [6] "Pectinacetylesterase"
## [7] "Tubulin C-terminal domain"
## [8] "Leucine rich repeat"
## [9] "Domain of unknown function (DUF4228)"
## [10] "AP2 domain"
## [11] "Cyclin, C-terminal domain"
## [12] "Tubulin/FtsZ family, GTPase domain"
## [13] "Multicopper oxidase"
## [14] "Pectate lyase"
## [15] "Multicopper oxidase"
## [16] "Cyclin, N-terminal domain"
## [17] "Multicopper oxidase"
## [18] "Glycosyl hydrolase family 9"
## [19] "Arabinogalactan peptide"
## [20] "(Dead): PF06548"
## [21] "Glycosyl hydrolases family 17"
## [22] "Protein of unknown function (DUF1005)"
## [23] "Hsp70 protein"
## [24] "Eukaryotic aspartyl protease"
## [25] "Targeting protein for Xklp2 (TPX2)"
## [26] "Plant protein of unknown function (DUF936)"
## [27] "Glycosyl transferase family group 2"
## [28] "Pollen allergen"
## [29] "Xylanase inhibitor C-terminal"
## [30] "Xylanase inhibitor N-terminal"
## [31] "Leucine Rich Repeat"
## [32] "Peroxidase"
## [33] "Lytic transglycolase"
## [34] "Calponin homology (CH) domain"
## [35] "Domain of unknown function (DUF3490)"
## [36] "Phosphate-induced protein 1 conserved region"
## [37] "Protein of unknown function (DUF1191)"
## [38] "C2H2-type zinc finger"
## [39] "Glycosyl hydrolase family 3 N terminal domain"
## [40] "Pectinesterase"
## [41] "UAA transporter family"
## [42] "HD-ZIP protein N terminus"
## [43] "Glycosyl hydrolase family 3 C-terminal domain"
## [44] "(Dead): PF12711"
## [45] "POT family"
## [46] "Protein kinase domain"
## [47] "Calreticulin family"
## [48] "Protein of unknown function (DUF642)"
## [49] "ADP-ribosylation factor family"
## [50] "Ribosome associated membrane protein RAMP4"
## [51] "Fn3-like domain"
## [52] "TPR repeat"
## [53] "Protein of unknown function (DUF1635)"
## [54] "EF-hand domain pair"
## [55] "Gibberellin regulated protein"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NSDMSO_Low <- GO
GO <- gopher(T6PKSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "liposaccharide metabolic process"
## [3] "membrane lipid metabolic process"
## [4] "response to light intensity"
## [5] "cell periphery"
## [6] "cell communication"
## [7] "protein folding"
## [8] "response to heat"
## [9] "lipid metabolic process"
## [10] "response to extracellular stimulus"
## [11] "cellular response to external stimulus"
## [12] "extracellular region"
## [13] "cellular response to phosphate starvation"
## [14] "response to drug"
## [15] "membrane"
## [16] "response to external stimulus"
## [17] "response to oxidative stress"
## [18] "vacuole"
## [19] "phosphate ion transmembrane transporter activity"
## [20] "external encapsulating structure"
## [21] "phosphate ion transport"
## [22] "acid phosphatase activity"
## [23] "response to antibiotic"
## [24] "cellular modified amino acid biosynthetic process"
## [25] "response to oxygen-containing compound"
## [26] "response to toxic substance"
## [27] "protein localization to membrane"
## [28] "endomembrane system"
## [29] "response to nitrogen compound"
## [30] "carbohydrate derivative biosynthetic process"
## [31] "hydrolase activity, acting on ester bonds"
## [32] "inorganic phosphate transmembrane transporter activity"
## [33] "amine metabolic process"
## [34] "external encapsulating structure organization"
## [35] "regulation of biological quality"
## [36] "symplast"
## [37] "cell junction"
## [38] "regulation of cell size"
## [39] "immune system process"
## [40] "cellular response to stimulus"
## [41] "polysaccharide localization"
## [42] "response to monosaccharide"
## [43] "multi-organism process"
## [44] "response to inorganic substance"
## [45] "negative regulation of cellular process"
## [46] "DNA binding"
## [47] "microtubule polymerization or depolymerization"
## [48] "protein localization to vacuole"
## [49] "aging"
## [50] "structural constituent of cell wall"
## [51] "cellular response to stress"
## [52] "transferase activity, transferring glycosyl groups"
## [53] "phosphoric ester hydrolase activity"
## [54] "localization"
## [55] "hydrolase activity"
## [56] "organic hydroxy compound metabolic process"
## [57] "carbohydrate derivative metabolic process"
## [58] "regulation of microtubule-based process"
## [59] "response to stress"
## [60] "carbohydrate metabolic process"
## [61] "drug metabolic process"
## [62] "cell development"
## [63] "response to chemical"
## [64] "cytoskeleton"
## [65] "negative regulation of biosynthetic process"
## [66] "galactosyltransferase activity"
## [67] "cellular macromolecule metabolic process"
## [68] "pollen development"
## [69] "response to wounding"
## [70] "sequence-specific DNA binding"
## [71] "response to endoplasmic reticulum stress"
## [72] "response to nutrient levels"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.2.1.151" "3.6.1.1" "3.1.4.46" "2.4.1.46"GO$pfam$name## [1] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [2] "Glycosyl hydrolases family 16"
## [3] "Purple acid Phosphatase, N-terminal domain"
## [4] "Iron/zinc purple acid phosphatase-like protein C"
## [5] "Glycerophosphoryl diester phosphodiesterase family"
## [6] "Calcineurin-like phosphoesterase"
## [7] "Hsp20/alpha crystallin family"
## [8] "AP2 domain"
## [9] "Major Facilitator Superfamily"
## [10] "C2H2-type zinc finger"
## [11] "Calreticulin family"
## [12] "Hsp70 protein"
## [13] "Sucrose synthase"
## [14] "EF-hand domain pair"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6PKSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6PKSDMSO_Low <- GO
GO <- gopher(T6NPDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "liposaccharide metabolic process"
## [3] "membrane lipid metabolic process"
## [4] "cell communication"
## [5] "response to light intensity"
## [6] "cellular response to external stimulus"
## [7] "response to extracellular stimulus"
## [8] "lipid metabolic process"
## [9] "cell periphery"
## [10] "protein folding"
## [11] "cellular response to phosphate starvation"
## [12] "cellular modified amino acid biosynthetic process"
## [13] "response to drug"
## [14] "extracellular region"
## [15] "response to oxidative stress"
## [16] "membrane"
## [17] "response to heat"
## [18] "vacuole"
## [19] "response to toxic substance"
## [20] "response to external stimulus"
## [21] "secondary metabolic process"
## [22] "aging"
## [23] "response to stress"
## [24] "response to inorganic substance"
## [25] "catabolic process"
## [26] "response to nitrogen compound"
## [27] "hydrolase activity, acting on ester bonds"
## [28] "phosphate ion transmembrane transporter activity"
## [29] "acid phosphatase activity"
## [30] "amine metabolic process"
## [31] "protein localization to vacuole"
## [32] "immune system process"
## [33] "regulation of biological quality"
## [34] "phosphate ion transport"
## [35] "inorganic phosphate transmembrane transporter activity"
## [36] "carbohydrate derivative biosynthetic process"
## [37] "endomembrane system organization"
## [38] "catalytic activity"
## [39] "response to antibiotic"
## [40] "response to temperature stimulus"
## [41] "carbohydrate derivative metabolic process"
## [42] "negative regulation of cellular process"
## [43] "negative regulation of biosynthetic process"
## [44] "plant epidermal cell differentiation"
## [45] "protein localization to membrane"
## [46] "endomembrane system"
## [47] "localization"
## [48] "cellular response to stimulus"
## [49] "hydrolase activity"
## [50] "response to wounding"
## [51] "chemical homeostasis"
## [52] "multi-organism process"
## [53] "transporter activity"
## [54] "benzene-containing compound metabolic process"
## [55] "response to oxygen-containing compound"
## [56] "polysaccharide localization"
## [57] "organic hydroxy compound metabolic process"
## [58] "carbohydrate metabolic process"
## [59] "ER-nucleus signaling pathway"
## [60] "postreplication repair"
## [61] "cellular macromolecule metabolic process"
## [62] "response to monosaccharide"
## [63] "cell development"
## [64] "cytoplasm"
## [65] "proteasomal protein catabolic process"
## [66] "regulation of meristem development"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.2.1.151"GO$pfam$name## [1] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [2] "Glycosyl hydrolases family 16"
## [3] "Purple acid Phosphatase, N-terminal domain"
## [4] "Iron/zinc purple acid phosphatase-like protein C"
## [5] "C2H2-type zinc finger"
## [6] "Calcineurin-like phosphoesterase"
## [7] "Glycerophosphoryl diester phosphodiesterase family"
## [8] "Calreticulin family"
## [9] "Universal stress protein family"
## [10] "Phosphatidylinositol-specific phospholipase C, X domain"
## [11] "Sucrose synthase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NPDMSO_Low <- GO9.2 T6 AZD
9.2.1 Induced genes
GO <- gopher(T6NPSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "thylakoid"
## [2] "plastid organization"
## [3] "photosynthesis"
## [4] "NADP metabolic process"
## [5] "glucose 6-phosphate metabolic process"
## [6] "organelle subcompartment"
## [7] "generation of precursor metabolites and energy"
## [8] "response to red light"
## [9] "secondary metabolic process"
## [10] "ion transport"
## [11] "protein localization to membrane"
## [12] "ribonucleoprotein complex biogenesis"
## [13] "tetrapyrrole metabolic process"
## [14] "response to stimulus"
## [15] "response to far red light"
## [16] "response to blue light"
## [17] "ncRNA metabolic process"
## [18] "biological regulation"
## [19] "protein-containing complex subunit organization"
## [20] "regulation of protein metabolic process"
## [21] "response to acid chemical"
## [22] "pigment metabolic process"
## [23] "light-harvesting complex"
## [24] "PSII associated light-harvesting complex II catabolic process"
## [25] "drug metabolic process"
## [26] "oxygen binding"
## [27] "response to oxygen-containing compound"
## [28] "oligosaccharide metabolic process"
## [29] "glycosyl compound metabolic process"
## [30] "immune system process"
## [31] "defense response"
## [32] "unsaturated fatty acid metabolic process"
## [33] "cofactor metabolic process"
## [34] "RNA metabolic process"
## [35] "tetrapyrrole binding"
## [36] "reactive oxygen species metabolic process"
## [37] "oxidation-reduction process"
## [38] "establishment of localization in cell"
## [39] "plastid"
## [40] "cell death"
## [41] "starch metabolic process"
## [42] "dephosphorylation"
## [43] "response to endogenous stimulus"
## [44] "serine family amino acid metabolic process"
## [45] "membrane organization"
## [46] "sulfur compound metabolic process"
## [47] "flavonoid metabolic process"
## [48] "transcription regulator activity"
## [49] "plastoglobule"
## [50] "cell communication"
## [51] "isoprenoid metabolic process"
## [52] "plastid envelope"
## [53] "response to biotic stimulus"
## [54] "multi-organism cellular process"
## [55] "organic acid metabolic process"
## [56] "rRNA metabolic process"
## [57] "amine metabolic process"
## [58] "small molecule biosynthetic process"
## [59] "shoot system morphogenesis"
## [60] "response to chemical"
## [61] "small nucleolar ribonucleoprotein complex"
## [62] "aging"
## [63] "oxidoreductase activity"
## [64] "leaf development"
## [65] "response to karrikin"
## [66] "single-stranded RNA binding"
## [67] "benzene-containing compound metabolic process"
## [68] "chemical homeostasis"
## [69] "regulation of seedling development"
## [70] "localization"
## [71] "indole-containing compound metabolic process"
## [72] "organic acid transport"
## [73] "DNA binding"
## [74] "cellular component biogenesis"
## [75] "sulfur compound biosynthetic process"
## [76] "response to disaccharide"
## [77] "phosphorus metabolic process"
## [78] "oxylipin metabolic process"
## [79] "vitamin metabolic process"
## [80] "organelle localization"
## [81] "multi-organism process"
## [82] "host programmed cell death induced by symbiont"
## [83] "plastid localization"
## [84] "multicellular organism development"
## [85] "apoplast"
## [86] "oxidoreduction coenzyme metabolic process"
## [87] "de-etiolation"
## [88] "cellular component assembly"
## [89] "organic hydroxy compound metabolic process"
## [90] "organic hydroxy compound biosynthetic process"
## [91] "cellular homeostasis"
## [92] "signaling"
## [93] "response to organic substance"
## [94] "organic cyclic compound biosynthetic process"
## [95] "carbon fixation"
## [96] "regulation of neurotransmitter levels"
## [97] "regulation of immune system process"
## [98] "microbody"
## [99] "regulation of multi-organism process"
## [100] "secondary active transmembrane transporter activity"
## [101] "photosynthesis, light reaction"
## [102] "photosystem"
## [103] "peptidyl-cysteine modification"
## [104] "aromatic compound biosynthetic process"
## [105] "membrane-bounded organelle"
## [106] "regulation of primary metabolic process"
## [107] "fat-soluble vitamin metabolic process"
## [108] "protein targeting"
## [109] "ER body"
## [110] "membrane"
## [111] "response to light stimulus"
## [112] "kinase activity"
## [113] "photosynthetic electron transport in photosystem I"
## [114] "protein repair"
## [115] "response to unfolded protein"
## [116] "positive regulation of molecular function"
## [117] "isopentenyl diphosphate metabolic process"
## [118] "protein modification process"
## [119] "cellular aldehyde metabolic process"
## [120] "tetraterpenoid metabolic process"
## [121] "oligopeptide transport"
## [122] "regulation of response to stimulus"
## [123] "rhythmic process"
## [124] "cellular component disassembly"
## [125] "axis specification"
## [126] "positive regulation of metabolic process"
## [127] "alpha-amino acid metabolic process"
## [128] "cofactor binding"
## [129] "lipid metabolic process"
## [130] "hyperosmotic response"GO$kegg$id## [1] "1.97.1.12" "3.1.1.1" "1.10.3.9" "2.7.7.59" "1.14.13.173"GO$pfam$name## [1] "Cytochrome P450"
## [2] "Chlorophyll A-B binding protein"
## [3] "PPR repeat family"
## [4] "PPR repeat"
## [5] "Leucine Rich Repeat"
## [6] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [7] "NB-ARC domain"
## [8] "Carboxylesterase family"
## [9] "Leucine rich repeat"
## [10] "Dimerisation domain"
## [11] "O-methyltransferase domain"
## [12] "GRAS domain family"
## [13] "MatE"
## [14] "CP12 domain"
## [15] "Myb-like DNA-binding domain"
## [16] "Leucine rich repeat N-terminal domain"
## [17] "von Willebrand factor type A domain"
## [18] "Jacalin-like lectin domain"
## [19] "Putative nuclear localisation signal"
## [20] "RING-like zinc finger"
## [21] "Late embryogenesis abundant (LEA) group 1"
## [22] "PsbP"
## [23] "non-haem dioxygenase in morphine synthesis N-terminal"
## [24] "Glycosyl hydrolase family 1"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NPSAZD_High <- GO
GO <- gopher(T6NSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "secondary metabolic process"
## [3] "thylakoid"
## [4] "plastid organization"
## [5] "protein localization to membrane"
## [6] "photosynthesis"
## [7] "ion transport"
## [8] "response to acid chemical"
## [9] "tetrapyrrole metabolic process"
## [10] "light-harvesting complex"
## [11] "flavonoid metabolic process"
## [12] "cell death"
## [13] "glucose 6-phosphate metabolic process"
## [14] "response to oxygen-containing compound"
## [15] "organelle subcompartment"
## [16] "immune system process"
## [17] "tetrapyrrole binding"
## [18] "multi-organism process"
## [19] "PSII associated light-harvesting complex II catabolic process"
## [20] "response to biotic stimulus"
## [21] "glycosyl compound metabolic process"
## [22] "cell communication"
## [23] "oxygen binding"
## [24] "response to red light"
## [25] "aging"
## [26] "pigment metabolic process"
## [27] "small molecule biosynthetic process"
## [28] "biological regulation"
## [29] "RNA metabolic process"
## [30] "indole-containing compound metabolic process"
## [31] "lipid metabolic process"
## [32] "drug metabolic process"
## [33] "plastid"
## [34] "organic acid metabolic process"
## [35] "NADP metabolic process"
## [36] "multi-organism cellular process"
## [37] "response to far red light"
## [38] "pigment catabolic process"
## [39] "organic acid transport"
## [40] "benzene-containing compound metabolic process"
## [41] "generation of precursor metabolites and energy"
## [42] "regulation of protein metabolic process"
## [43] "response to chemical"
## [44] "protein-containing complex subunit organization"
## [45] "protein targeting"
## [46] "starch metabolic process"
## [47] "extracellular region"
## [48] "response to blue light"
## [49] "response to endogenous stimulus"
## [50] "dephosphorylation"
## [51] "catabolic process"
## [52] "response to external stimulus"
## [53] "localization"
## [54] "sulfur compound metabolic process"
## [55] "cellular homeostasis"
## [56] "cofactor binding"
## [57] "defense response"
## [58] "plastid envelope"
## [59] "membrane-bounded organelle"
## [60] "sulfur compound biosynthetic process"
## [61] "oligosaccharide metabolic process"
## [62] "reactive oxygen species metabolic process"
## [63] "serine family amino acid metabolic process"
## [64] "regulation of multi-organism process"
## [65] "plastoglobule"
## [66] "response to wounding"
## [67] "DNA binding"
## [68] "amine metabolic process"
## [69] "response to fungus"
## [70] "single-stranded RNA binding"
## [71] "oxidoreductase activity"
## [72] "cofactor metabolic process"
## [73] "organic hydroxy compound metabolic process"
## [74] "regulation of response to stimulus"
## [75] "regulation of immune system process"
## [76] "UDP-glycosyltransferase activity"
## [77] "detoxification"
## [78] "ribonucleoprotein complex biogenesis"
## [79] "hyperosmotic salinity response"
## [80] "organic hydroxy compound biosynthetic process"
## [81] "signaling"
## [82] "cellular response to environmental stimulus"
## [83] "oxidation-reduction process"
## [84] "chemical homeostasis"
## [85] "oxidoreduction coenzyme metabolic process"
## [86] "aromatic compound biosynthetic process"
## [87] "organic cyclic compound biosynthetic process"
## [88] "unsaturated fatty acid metabolic process"
## [89] "organic cyclic compound catabolic process"
## [90] "response to light stimulus"
## [91] "ncRNA metabolic process"
## [92] "regulation of seedling development"
## [93] "response to karrikin"
## [94] "de-etiolation"
## [95] "peptidase regulator activity"
## [96] "organic acid catabolic process"
## [97] "regulation of biological quality"
## [98] "response to inorganic substance"
## [99] "shoot system morphogenesis"
## [100] "peptidyl-cysteine modification"
## [101] "cellular nitrogen compound catabolic process"
## [102] "ER body"
## [103] "response to osmotic stress"
## [104] "transcription regulator activity"
## [105] "heterocycle biosynthetic process"
## [106] "cellular component disassembly"
## [107] "ATPase activity"
## [108] "leaf development"
## [109] "response to nitrogen compound"
## [110] "protein repair"
## [111] "organonitrogen compound catabolic process"
## [112] "response to disaccharide"
## [113] "glutathione transferase activity"
## [114] "protein modification process"
## [115] "small molecule metabolic process"
## [116] "regulation of flavonoid biosynthetic process"
## [117] "multicellular organism development"
## [118] "membrane"
## [119] "microbody"
## [120] "response to oxygen radical"
## [121] "kinase activity"
## [122] "cellular component biogenesis"
## [123] "intramolecular lyase activity"
## [124] "response to stress"
## [125] "vacuole"
## [126] "aromatic amino acid family metabolic process"
## [127] "fatty acid derivative metabolic process"
## [128] "hormone metabolic process"
## [129] "host programmed cell death induced by symbiont"
## [130] "male gamete generation"
## [131] "cellular amino acid metabolic process"
## [132] "response to organic substance"GO$kegg$id## [1] "1.10.3.9" "1.97.1.12" "3.1.1.1"GO$pfam$name## [1] "Chlorophyll A-B binding protein"
## [2] "Cytochrome P450"
## [3] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [4] "No apical meristem (NAM) protein"
## [5] "Dimerisation domain"
## [6] "non-haem dioxygenase in morphine synthesis N-terminal"
## [7] "O-methyltransferase domain"
## [8] "Carboxylesterase family"
## [9] "2OG-Fe(II) oxygenase superfamily"
## [10] "Leucine Rich Repeat"
## [11] "Dehydrin"
## [12] "Leucine rich repeat"
## [13] "CP12 domain"
## [14] "Ring finger domain"
## [15] "MatE"
## [16] "Zinc-binding dehydrogenase"
## [17] "Protein of unknown function (DUF563)"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NSAZD_High <- GO
GO <- gopher(T6PKSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "plastid organization"
## [2] "thylakoid"
## [3] "photosynthesis"
## [4] "glucose 6-phosphate metabolic process"
## [5] "secondary metabolic process"
## [6] "NADP metabolic process"
## [7] "protein localization to membrane"
## [8] "ion transport"
## [9] "organelle subcompartment"
## [10] "response to stimulus"
## [11] "response to red light"
## [12] "generation of precursor metabolites and energy"
## [13] "response to far red light"
## [14] "response to acid chemical"
## [15] "ribonucleoprotein complex biogenesis"
## [16] "regulation of protein metabolic process"
## [17] "immune system process"
## [18] "defense response"
## [19] "light-harvesting complex"
## [20] "biological regulation"
## [21] "tetrapyrrole metabolic process"
## [22] "plastid"
## [23] "oxygen binding"
## [24] "cell death"
## [25] "protein-containing complex subunit organization"
## [26] "RNA metabolic process"
## [27] "response to oxygen-containing compound"
## [28] "amine metabolic process"
## [29] "glycosyl compound metabolic process"
## [30] "drug metabolic process"
## [31] "pigment metabolic process"
## [32] "response to blue light"
## [33] "indole-containing compound metabolic process"
## [34] "response to karrikin"
## [35] "response to biotic stimulus"
## [36] "oligosaccharide metabolic process"
## [37] "reactive oxygen species metabolic process"
## [38] "flavonoid metabolic process"
## [39] "transcription regulator activity"
## [40] "ncRNA metabolic process"
## [41] "localization"
## [42] "multi-organism cellular process"
## [43] "single-stranded RNA binding"
## [44] "PSII associated light-harvesting complex II catabolic process"
## [45] "tetrapyrrole binding"
## [46] "small molecule biosynthetic process"
## [47] "shoot system morphogenesis"
## [48] "unsaturated fatty acid metabolic process"
## [49] "cell communication"
## [50] "cofactor metabolic process"
## [51] "membrane organization"
## [52] "sulfur compound metabolic process"
## [53] "multi-organism process"
## [54] "alpha-amino acid metabolic process"
## [55] "plastoglobule"
## [56] "oxidation-reduction process"
## [57] "rRNA metabolic process"
## [58] "starch metabolic process"
## [59] "organic acid metabolic process"
## [60] "plastid envelope"
## [61] "aging"
## [62] "dephosphorylation"
## [63] "oligopeptide transport"
## [64] "oxidoreductase activity"
## [65] "response to chemical"
## [66] "sulfur compound biosynthetic process"
## [67] "DNA binding"
## [68] "leaf development"
## [69] "extracellular region"
## [70] "cellular homeostasis"
## [71] "regulation of multi-organism process"
## [72] "response to disaccharide"
## [73] "membrane"
## [74] "serine family amino acid metabolic process"
## [75] "response to nitrogen compound"
## [76] "chemical homeostasis"
## [77] "host programmed cell death induced by symbiont"
## [78] "organic cyclic compound biosynthetic process"
## [79] "establishment of localization in cell"
## [80] "apoplast"
## [81] "protein targeting"
## [82] "regulation of immune system process"
## [83] "regulation of response to stimulus"
## [84] "organic acid transport"
## [85] "response to unfolded protein"
## [86] "aromatic compound biosynthetic process"
## [87] "benzene-containing compound metabolic process"
## [88] "phosphorus metabolic process"
## [89] "drug binding"
## [90] "regulation of seedling development"
## [91] "response to external stimulus"
## [92] "response to endogenous stimulus"
## [93] "multicellular organism development"
## [94] "organic hydroxy compound metabolic process"
## [95] "vitamin metabolic process"
## [96] "isoprenoid metabolic process"
## [97] "microbody"
## [98] "glutathione transferase activity"
## [99] "detoxification"
## [100] "cellular component biogenesis"
## [101] "energy quenching"
## [102] "lipase activity"
## [103] "positive regulation of metabolic process"
## [104] "signaling"
## [105] "reactive nitrogen species metabolic process"
## [106] "photosynthesis, light reaction"
## [107] "kinase activity"
## [108] "nitrogen cycle metabolic process"
## [109] "oxidoreduction coenzyme metabolic process"
## [110] "cellular component assembly"
## [111] "oxylipin metabolic process"
## [112] "regulation of primary metabolic process"
## [113] "photosystem"
## [114] "membrane-bounded organelle"
## [115] "cellular hormone metabolic process"
## [116] "cofactor binding"
## [117] "response to organic cyclic compound"
## [118] "organonitrogen compound catabolic process"
## [119] "regulation of neurotransmitter levels"
## [120] "adenyl nucleotide binding"
## [121] "regulation of molecular function"
## [122] "envelope"
## [123] "carbon fixation"
## [124] "protein modification process"
## [125] "bract development"
## [126] "lipid metabolic process"
## [127] "cyclic nucleotide binding"
## [128] "organic hydroxy compound biosynthetic process"
## [129] "response to light stimulus"
## [130] "chlorophyll metabolic process"
## [131] "intramolecular lyase activity"
## [132] "O-acyltransferase activity"
## [133] "organic acid catabolic process"GO$kegg$id## [1] "1.97.1.12" "3.1.1.1" "1.10.3.9" "2.5.1.18" "2.7.11.1"
## [6] "1.14.13.173" "2.4.2.51" "2.8.2.24" "3.2.1.14" "3.1.1.3"
## [11] "1.3.3.8" "2.7.7.59" "1.2.1.13"GO$pfam$name## [1] "Cytochrome P450"
## [2] "Chlorophyll A-B binding protein"
## [3] "Leucine Rich Repeat"
## [4] "Dimerisation domain"
## [5] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [6] "NB-ARC domain"
## [7] "von Willebrand factor type A domain"
## [8] "O-methyltransferase domain"
## [9] "Myb-like DNA-binding domain"
## [10] "RING-like zinc finger"
## [11] "Carboxylesterase family"
## [12] "Protein kinase domain"
## [13] "WRKY DNA -binding domain"
## [14] "Leucine rich repeat"
## [15] "Leucine rich repeat N-terminal domain"
## [16] "Jacalin-like lectin domain"
## [17] "Glutathione S-transferase, C-terminal domain"
## [18] "zinc-finger of the FCS-type, C2-C2"
## [19] "Legume lectin domain"
## [20] "POT family"
## [21] "D-mannose binding lectin"
## [22] "Putative nuclear localisation signal"
## [23] "Domain of unknown function (DUF1338)"
## [24] "non-haem dioxygenase in morphine synthesis N-terminal"
## [25] "Glutamine synthetase, beta-Grasp domain"
## [26] "Berberine and berberine like"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6PKSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T6PKSAZD_High <- GO
GO <- gopher(T6NPAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "thylakoid"
## [2] "plastid organization"
## [3] "photosynthesis"
## [4] "organelle subcompartment"
## [5] "NADP metabolic process"
## [6] "secondary metabolic process"
## [7] "glucose 6-phosphate metabolic process"
## [8] "ion transport"
## [9] "generation of precursor metabolites and energy"
## [10] "ribonucleoprotein complex biogenesis"
## [11] "response to red light"
## [12] "protein localization to membrane"
## [13] "response to stimulus"
## [14] "ncRNA metabolic process"
## [15] "tetrapyrrole metabolic process"
## [16] "response to far red light"
## [17] "biological regulation"
## [18] "response to acid chemical"
## [19] "light-harvesting complex"
## [20] "defense response"
## [21] "response to blue light"
## [22] "pigment metabolic process"
## [23] "regulation of protein metabolic process"
## [24] "response to oxygen-containing compound"
## [25] "oxygen binding"
## [26] "glycosyl compound metabolic process"
## [27] "immune system process"
## [28] "protein-containing complex subunit organization"
## [29] "amine metabolic process"
## [30] "RNA metabolic process"
## [31] "tetrapyrrole binding"
## [32] "plastid"
## [33] "membrane organization"
## [34] "PSII associated light-harvesting complex II catabolic process"
## [35] "starch metabolic process"
## [36] "organic acid metabolic process"
## [37] "oligosaccharide metabolic process"
## [38] "oxidation-reduction process"
## [39] "cell death"
## [40] "drug metabolic process"
## [41] "serine family amino acid metabolic process"
## [42] "establishment of localization in cell"
## [43] "sulfur compound metabolic process"
## [44] "unsaturated fatty acid metabolic process"
## [45] "extracellular region"
## [46] "response to biotic stimulus"
## [47] "response to karrikin"
## [48] "shoot system morphogenesis"
## [49] "dephosphorylation"
## [50] "organic acid transport"
## [51] "leaf development"
## [52] "reactive oxygen species metabolic process"
## [53] "isoprenoid metabolic process"
## [54] "aging"
## [55] "flavonoid metabolic process"
## [56] "rRNA metabolic process"
## [57] "multi-organism cellular process"
## [58] "chemical homeostasis"
## [59] "oxidoreductase activity"
## [60] "indole-containing compound metabolic process"
## [61] "cell communication"
## [62] "localization"
## [63] "cofactor metabolic process"
## [64] "response to endogenous stimulus"
## [65] "plastid envelope"
## [66] "phosphorus metabolic process"
## [67] "multi-organism process"
## [68] "small nucleolar ribonucleoprotein complex"
## [69] "carbon fixation"
## [70] "DNA binding"
## [71] "single-stranded RNA binding"
## [72] "ER body"
## [73] "oligopeptide transport"
## [74] "response to disaccharide"
## [75] "cellular aldehyde metabolic process"
## [76] "transcription regulator activity"
## [77] "sulfur compound biosynthetic process"
## [78] "response to chemical"
## [79] "plastoglobule"
## [80] "cellular homeostasis"
## [81] "oxidoreduction coenzyme metabolic process"
## [82] "plastid localization"
## [83] "regulation of primary metabolic process"
## [84] "response to unfolded protein"
## [85] "drug binding"
## [86] "membrane"
## [87] "organelle localization"
## [88] "cellular component biogenesis"
## [89] "regulation of neurotransmitter levels"
## [90] "cofactor binding"
## [91] "response to external stimulus"
## [92] "response to wounding"
## [93] "regulation of multi-organism process"
## [94] "vitamin metabolic process"
## [95] "small molecule biosynthetic process"
## [96] "response to light stimulus"
## [97] "kinase activity"
## [98] "apoplast"
## [99] "aromatic compound biosynthetic process"
## [100] "isopentenyl diphosphate metabolic process"
## [101] "ligase activity, forming nitrogen-metal bonds"
## [102] "organic cyclic compound biosynthetic process"
## [103] "benzene-containing compound metabolic process"
## [104] "regulation of immune system process"
## [105] "membrane-bounded organelle"
## [106] "oxylipin metabolic process"
## [107] "regulation of response to stimulus"
## [108] "signaling"
## [109] "alpha-amino acid metabolic process"
## [110] "small molecule metabolic process"
## [111] "lipid metabolic process"
## [112] "cellular component assembly"
## [113] "positive regulation of molecular function"
## [114] "multicellular organism development"
## [115] "protein targeting"
## [116] "envelope"
## [117] "host programmed cell death induced by symbiont"
## [118] "lipase activity"
## [119] "regulation of molecular function"
## [120] "carbohydrate derivative metabolic process"
## [121] "protein modification process"
## [122] "response to nitrogen compound"
## [123] "O-methyltransferase activity"
## [124] "bract development"
## [125] "response to organic substance"
## [126] "photosynthetic membrane"
## [127] "photosynthetic electron transport in photosystem I"
## [128] "post-embryonic plant morphogenesis"
## [129] "microbody"
## [130] "positive regulation of metabolic process"
## [131] "photosystem"
## [132] "detoxification"
## [133] "defense response, incompatible interaction"
## [134] "protein domain specific binding"
## [135] "plastid stroma"
## [136] "hyperosmotic response"GO$kegg$id## [1] "1.97.1.12" "1.10.3.9" "3.1.1.1" "2.4.2.51" "1.2.1.13" "1.3.3.8"
## [7] "2.8.2.24" "2.5.1.18" "2.6.1.44" "2.3.1.199" "2.7.7.59"GO$pfam$name## [1] "Cytochrome P450"
## [2] "Chlorophyll A-B binding protein"
## [3] "Dimerisation domain"
## [4] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [5] "O-methyltransferase domain"
## [6] "Leucine Rich Repeat"
## [7] "NB-ARC domain"
## [8] "WRKY DNA -binding domain"
## [9] "Jacalin-like lectin domain"
## [10] "von Willebrand factor type A domain"
## [11] "PPR repeat"
## [12] "RING-like zinc finger"
## [13] "non-haem dioxygenase in morphine synthesis N-terminal"
## [14] "CP12 domain"
## [15] "PPR repeat family"
## [16] "2OG-Fe(II) oxygenase superfamily"
## [17] "Glycosyl hydrolase family 1"
## [18] "Carboxylesterase family"
## [19] "D-mannose binding lectin"
## [20] "PsbP"
## [21] "Leucine rich repeat"
## [22] "Berberine and berberine like"
## [23] "Myb-like DNA-binding domain"
## [24] "Protein kinase domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T6NPAZD_High <- GO9.2.2 Repressed genes
GO <- gopher(T6NPSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "extracellular region"
## [3] "endomembrane system"
## [4] "membrane"
## [5] "symplast"
## [6] "cell junction"
## [7] "membrane lipid metabolic process"
## [8] "response to light intensity"
## [9] "response to heat"
## [10] "external encapsulating structure"
## [11] "carbohydrate metabolic process"
## [12] "protein folding"
## [13] "liposaccharide metabolic process"
## [14] "response to stimulus"
## [15] "purine-containing compound metabolic process"
## [16] "growth"
## [17] "external encapsulating structure organization"
## [18] "cell wall organization or biogenesis"
## [19] "cell communication"
## [20] "cytoskeleton organization"
## [21] "nucleoside bisphosphate metabolic process"
## [22] "vacuole"
## [23] "thioester metabolic process"
## [24] "cellular response to phosphate starvation"
## [25] "lipid metabolic process"
## [26] "response to oxidative stress"
## [27] "regulation of biological quality"
## [28] "acid phosphatase activity"
## [29] "organic hydroxy compound metabolic process"
## [30] "response to endoplasmic reticulum stress"
## [31] "cellular response to external stimulus"
## [32] "response to extracellular stimulus"
## [33] "cell development"
## [34] "tubulin complex"
## [35] "transferase activity, transferring glycosyl groups"
## [36] "vesicle"
## [37] "intrinsic component of membrane"
## [38] "regulation of meristem development"
## [39] "hydrolase activity, acting on glycosyl bonds"
## [40] "copper ion binding"
## [41] "anchored component of membrane"
## [42] "response to drug"
## [43] "root system development"
## [44] "carbohydrate derivative metabolic process"
## [45] "sulfur compound metabolic process"
## [46] "structural constituent of cytoskeleton"
## [47] "cytoskeleton"
## [48] "small molecule metabolic process"
## [49] "ribose phosphate metabolic process"
## [50] "coenzyme metabolic process"
## [51] "cytoplasm"
## [52] "phosphate ion transmembrane transporter activity"
## [53] "response to mechanical stimulus"
## [54] "polysaccharide localization"
## [55] "protein polymerization"
## [56] "pigmentation"
## [57] "response to external stimulus"
## [58] "plant epidermal cell differentiation"
## [59] "regulation of cell size"
## [60] "negative regulation of cellular process"
## [61] "phosphate ion transport"
## [62] "response to monosaccharide"
## [63] "cellular response to stimulus"
## [64] "tissue development"
## [65] "organonitrogen compound metabolic process"
## [66] "proteasomal protein catabolic process"
## [67] "response to antibiotic"
## [68] "inorganic phosphate transmembrane transporter activity"
## [69] "negative regulation of biosynthetic process"
## [70] "multidimensional cell growth"
## [71] "microtubule-based process"
## [72] "nucleobase-containing small molecule metabolic process"
## [73] "meristem maintenance"
## [74] "protein localization to membrane"
## [75] "multi-multicellular organism process"
## [76] "chromosomal region"
## [77] "galacturonan metabolic process"
## [78] "response to brassinosteroid"
## [79] "cellular component morphogenesis"
## [80] "response to nitrogen compound"
## [81] "root hair cell development"
## [82] "beta-glucan metabolic process"
## [83] "DNA binding"
## [84] "drug metabolic process"
## [85] "response to toxic substance"
## [86] "nucleobase-containing compound kinase activity"
## [87] "response to oxygen-containing compound"
## [88] "intramolecular oxidoreductase activity"
## [89] "cellular response to stress"
## [90] "response to inorganic substance"
## [91] "cellular modified amino acid biosynthetic process"
## [92] "steroid metabolic process"
## [93] "phosphoric ester hydrolase activity"
## [94] "syncytium formation"
## [95] "structural constituent of cell wall"
## [96] "chemical homeostasis"
## [97] "catalytic activity"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.6.1.1" "3.4.23.12" "3.2.1.151" "2.4.2.1"
## [7] "5.3.4.1" "1.11.1.7" "2.4.1.46" "1.10.3.3" "3.2.1.39" "3.1.4.46"
## [13] "3.2.1.4"GO$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "Tubulin C-terminal domain"
## [4] "Purple acid Phosphatase, N-terminal domain"
## [5] "Tubulin/FtsZ family, GTPase domain"
## [6] "Fasciclin domain"
## [7] "Iron/zinc purple acid phosphatase-like protein C"
## [8] "Glycerophosphoryl diester phosphodiesterase family"
## [9] "Calcineurin-like phosphoesterase"
## [10] "Thioredoxin-like domain"
## [11] "Major Facilitator Superfamily"
## [12] "Glycosyl hydrolases family 17"
## [13] "Eukaryotic aspartyl protease"
## [14] "Arabinogalactan peptide"
## [15] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [16] "Leucine rich repeat N-terminal domain"
## [17] "Glycosyl hydrolase family 9"
## [18] "GDP-fucose protein O-fucosyltransferase"
## [19] "Calreticulin family"
## [20] "Protein of unknown function (DUF1005)"
## [21] "AP2 domain"
## [22] "Domain of unknown function (DUF4228)"
## [23] "Hsp70 protein"
## [24] "Multicopper oxidase"
## [25] "Lytic transglycolase"
## [26] "Hsp20/alpha crystallin family"
## [27] "Glycosyl transferase family 8"
## [28] "Multicopper oxidase"
## [29] "Multicopper oxidase"
## [30] "Profilin"
## [31] "Gibberellin regulated protein"
## [32] "Pectinacetylesterase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NPSAZD_Low <- GO
GO <- gopher(T6NSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "structural molecule activity"
## [2] "non-membrane-bounded organelle"
## [3] "methylation"
## [4] "cell periphery"
## [5] "symplast"
## [6] "cell junction"
## [7] "cellular amide metabolic process"
## [8] "microtubule-based process"
## [9] "external encapsulating structure"
## [10] "ribonucleoprotein complex"
## [11] "steroid metabolic process"
## [12] "membrane"
## [13] "extracellular region"
## [14] "endomembrane system"
## [15] "ribose phosphate metabolic process"
## [16] "cytosol"
## [17] "protein alkylation"
## [18] "nucleobase-containing small molecule metabolic process"
## [19] "organonitrogen compound metabolic process"
## [20] "DNA replication"
## [21] "cytoskeleton organization"
## [22] "response to heat"
## [23] "cellular component organization or biogenesis"
## [24] "cell population proliferation"
## [25] "thioester metabolic process"
## [26] "growth"
## [27] "peptidyl-amino acid modification"
## [28] "vacuole"
## [29] "anchored component of membrane"
## [30] "protein folding"
## [31] "cell wall organization or biogenesis"
## [32] "response to light intensity"
## [33] "flower calyx development"
## [34] "cell division"
## [35] "ribosome"
## [36] "response to endoplasmic reticulum stress"
## [37] "hydrolase activity, acting on glycosyl bonds"
## [38] "coenzyme metabolic process"
## [39] "copper ion binding"
## [40] "membrane-enclosed lumen"
## [41] "regulation of meristem development"
## [42] "protein-containing complex"
## [43] "tubulin complex"
## [44] "intrinsic component of membrane"
## [45] "organelle assembly"
## [46] "cell cycle phase transition"
## [47] "regulation of gene expression, epigenetic"
## [48] "motor activity"
## [49] "corolla development"
## [50] "regulation of developmental process"
## [51] "negative regulation of gene expression, epigenetic"
## [52] "response to mechanical stimulus"
## [53] "cellular macromolecule metabolic process"
## [54] "ribosomal small subunit biogenesis"
## [55] "multidimensional cell growth"
## [56] "pyrimidine-containing compound metabolic process"
## [57] "external encapsulating structure organization"
## [58] "response to oxidative stress"
## [59] "cell cycle"
## [60] "RNA modification"
## [61] "root hair cell development"
## [62] "gene silencing"
## [63] "meristem maintenance"
## [64] "protein polymerization"
## [65] "regulation of cell cycle"
## [66] "anatomical structure formation involved in morphogenesis"
## [67] "cytokinesis"
## [68] "nucleoside bisphosphate metabolic process"
## [69] "response to brassinosteroid"
## [70] "macromolecule modification"
## [71] "chromatin organization"
## [72] "response to cyclopentenone"
## [73] "plant-type cell wall organization or biogenesis"
## [74] "chromatin organization involved in regulation of transcription"
## [75] "mitotic cell cycle process"
## [76] "pigmentation"
## [77] "galacturonan metabolic process"
## [78] "negative regulation of cellular process"
## [79] "syncytium formation"
## [80] "phosphorus metabolic process"
## [81] "post-embryonic plant organ development"
## [82] "cytoplasm"
## [83] "chromosome organization"
## [84] "kinase regulator activity"
## [85] "carboxylic ester hydrolase activity"
## [86] "vesicle"
## [87] "carbohydrate derivative binding"
## [88] "tissue development"
## [89] "nucleoside phosphate binding"
## [90] "response to monosaccharide"
## [91] "biosynthetic process"
## [92] "proteasomal protein catabolic process"
## [93] "plant-type cell wall loosening"
## [94] "phragmoplast"
## [95] "rRNA transport"
## [96] "regulation of growth"
## [97] "rRNA-containing ribonucleoprotein complex export from nucleus"
## [98] "organic substance metabolic process"
## [99] "carbon-oxygen lyase activity, acting on polysaccharides"
## [100] "protein localization to nucleus"
## [101] "bounding membrane of organelle"
## [102] "beta-glucan metabolic process"
## [103] "plant organ morphogenesis"GO$kegg$id## [1] "2.4.1.207" "3.6.4.4" "1.10.3.3" "3.4.23.12" "2.4.99.18" "2.4.2.1"
## [7] "3.2.1.4" "3.2.1.151" "3.2.1.39" "4.2.2.2" "3.6.4.5"GO$pfam$name## [1] "Tubulin C-terminal domain"
## [2] "Cyclin, C-terminal domain"
## [3] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [4] "Kinesin motor domain"
## [5] "Tubulin/FtsZ family, GTPase domain"
## [6] "Glycosyl hydrolases family 16"
## [7] "Cyclin, N-terminal domain"
## [8] "Fasciclin domain"
## [9] "Leucine rich repeat N-terminal domain"
## [10] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [11] "Eukaryotic aspartyl protease"
## [12] "Glycosyl hydrolases family 17"
## [13] "Multicopper oxidase"
## [14] "Pollen allergen"
## [15] "Multicopper oxidase"
## [16] "Multicopper oxidase"
## [17] "Glycosyl hydrolase family 9"
## [18] "Lytic transglycolase"
## [19] "Arabinogalactan peptide"
## [20] "Glycosyl transferase family group 2"
## [21] "Protein of unknown function (DUF1005)"
## [22] "Ribosomal protein L6"
## [23] "Pectate lyase"
## [24] "X8 domain"
## [25] "Calreticulin family"
## [26] "Domain of unknown function (DUF4228)"
## [27] "Calponin homology (CH) domain"
## [28] "RS4NT (NUC023) domain"
## [29] "EB1-like C-terminal motif"
## [30] "Targeting protein for Xklp2 (TPX2)"
## [31] "40S ribosomal protein S4 C-terminus"
## [32] "Mitochondrial ATP synthase g subunit"
## [33] "Ribosomal family S4e"
## [34] "Xylanase inhibitor C-terminal"
## [35] "60s Acidic ribosomal protein"
## [36] "Plant protein of unknown function (DUF936)"
## [37] "Hsp70 protein"
## [38] "Protein of unknown function (DUF642)"
## [39] "KOW motif"
## [40] "UAA transporter family"
## [41] "Hsp90 protein"
## [42] "Ribosomal protein L35Ae"
## [43] "(Dead): PF06548"
## [44] "UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain"
## [45] "UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain"
## [46] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [47] "Pectinacetylesterase"
## [48] "Ribosomal protein L23"
## [49] "Ribosomal protein S2"
## [50] "UDP-glucose/GDP-mannose dehydrogenase family, central domain"
## [51] "Tim10/DDP family zinc finger"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NSAZD_Low <- GO
GO <- gopher(T6PKSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "extracellular region"
## [3] "membrane lipid metabolic process"
## [4] "membrane"
## [5] "response to light intensity"
## [6] "liposaccharide metabolic process"
## [7] "protein folding"
## [8] "endomembrane system"
## [9] "response to heat"
## [10] "symplast"
## [11] "cell junction"
## [12] "external encapsulating structure"
## [13] "response to stimulus"
## [14] "carbohydrate metabolic process"
## [15] "response to oxidative stress"
## [16] "cellular response to phosphate starvation"
## [17] "cell communication"
## [18] "cellular response to external stimulus"
## [19] "vacuole"
## [20] "response to extracellular stimulus"
## [21] "response to endoplasmic reticulum stress"
## [22] "external encapsulating structure organization"
## [23] "response to drug"
## [24] "cell wall organization or biogenesis"
## [25] "response to mechanical stimulus"
## [26] "transferase activity, transferring glycosyl groups"
## [27] "purine-containing compound metabolic process"
## [28] "response to external stimulus"
## [29] "copper ion binding"
## [30] "lipid metabolic process"
## [31] "carbohydrate derivative metabolic process"
## [32] "hydrolase activity, acting on glycosyl bonds"
## [33] "phosphate ion transport"
## [34] "response to antibiotic"
## [35] "growth"
## [36] "response to toxic substance"
## [37] "anchored component of membrane"
## [38] "acid phosphatase activity"
## [39] "response to monosaccharide"
## [40] "inorganic phosphate transmembrane transporter activity"
## [41] "small molecule metabolic process"
## [42] "regulation of meristem development"
## [43] "phosphate ion transmembrane transporter activity"
## [44] "cellular response to stress"
## [45] "root system development"
## [46] "regulation of biological quality"
## [47] "intrinsic component of membrane"
## [48] "root hair cell development"
## [49] "cytoplasm"
## [50] "organic hydroxy compound metabolic process"
## [51] "transporter activity"
## [52] "regulation of cell size"
## [53] "response to oxygen-containing compound"
## [54] "polysaccharide localization"
## [55] "cellular response to stimulus"
## [56] "vesicle"
## [57] "cytoskeleton organization"
## [58] "hydrolase activity"
## [59] "cell development"
## [60] "oligosaccharide biosynthetic process"
## [61] "defense response, incompatible interaction"
## [62] "organophosphate ester transport"
## [63] "ion binding"
## [64] "apoplast"
## [65] "meristem maintenance"
## [66] "response to temperature stimulus"
## [67] "thioester metabolic process"
## [68] "cellular metabolic compound salvage"
## [69] "negative regulation of biosynthetic process"
## [70] "antioxidant activity"
## [71] "nucleobase-containing compound kinase activity"
## [72] "response to disaccharide"
## [73] "response to inorganic substance"
## [74] "proteasomal protein catabolic process"
## [75] "oxidoreductase activity, acting on peroxide as acceptor"
## [76] "protein localization to membrane"
## [77] "plant epidermal cell differentiation"
## [78] "cellular macromolecule metabolic process"
## [79] "response to nitrogen compound"
## [80] "galactosyltransferase activity"
## [81] "phosphoric ester hydrolase activity"
## [82] "nucleoside bisphosphate metabolic process"
## [83] "negative regulation of cellular process"
## [84] "chemical homeostasis"
## [85] "ER-nucleus signaling pathway"
## [86] "syncytium formation"
## [87] "response to stress"
## [88] "nucleobase-containing small molecule metabolic process"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.6.1.1" "1.11.1.7" "3.2.1.151" "3.4.23.12"
## [7] "1.10.3.3" "3.1.4.46" "2.4.1.46" "5.3.4.1"GO$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "Hsp20/alpha crystallin family"
## [4] "Purple acid Phosphatase, N-terminal domain"
## [5] "Glycerophosphoryl diester phosphodiesterase family"
## [6] "Fasciclin domain"
## [7] "Iron/zinc purple acid phosphatase-like protein C"
## [8] "Calcineurin-like phosphoesterase"
## [9] "Hsp70 protein"
## [10] "Thioredoxin-like domain"
## [11] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [12] "Calreticulin family"
## [13] "Major Facilitator Superfamily"
## [14] "Peroxidase"
## [15] "Multicopper oxidase"
## [16] "PDDEXK-like family of unknown function"
## [17] "Eukaryotic aspartyl protease"
## [18] "Glycosyl hydrolase family 9"
## [19] "Multicopper oxidase"
## [20] "UAA transporter family"
## [21] "Multicopper oxidase"
## [22] "EF-hand domain pair"
## [23] "EF-hand domain pair"
## [24] "ZIP Zinc transporter"
## [25] "AP2 domain"
## [26] "Glycosyl hydrolases family 17"
## [27] "Profilin"
## [28] "Tubulin C-terminal domain"
## [29] "Gibberellin regulated protein"
## [30] "Pectinacetylesterase"
## [31] "Xylanase inhibitor C-terminal"
## [32] "Phosphoenolpyruvate carboxylase"
## [33] "Glycosyltransferase family 28 C-terminal domain"
## [34] "Arabinogalactan peptide"
## [35] "Glycosyl transferase family 8"
## [36] "Centromere kinetochore component CENP-T histone fold"
## [37] "Tubulin/FtsZ family, GTPase domain"
## [38] "Pollen proteins Ole e I like"
## [39] "PLAT/LH2 domain"
## [40] "C2H2-type zinc finger"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6PKSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6PKSAZD_Low <- GO
GO <- gopher(T6NPAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "membrane lipid metabolic process"
## [3] "extracellular region"
## [4] "liposaccharide metabolic process"
## [5] "response to light intensity"
## [6] "protein folding"
## [7] "membrane"
## [8] "endomembrane system"
## [9] "response to heat"
## [10] "response to stimulus"
## [11] "external encapsulating structure"
## [12] "carbohydrate metabolic process"
## [13] "cellular response to phosphate starvation"
## [14] "cell communication"
## [15] "cellular response to external stimulus"
## [16] "response to extracellular stimulus"
## [17] "purine-containing compound metabolic process"
## [18] "symplast"
## [19] "cell junction"
## [20] "response to oxidative stress"
## [21] "lipid metabolic process"
## [22] "external encapsulating structure organization"
## [23] "response to endoplasmic reticulum stress"
## [24] "vacuole"
## [25] "carbohydrate derivative metabolic process"
## [26] "response to drug"
## [27] "phosphate ion transport"
## [28] "response to external stimulus"
## [29] "hydrolase activity, acting on glycosyl bonds"
## [30] "cell wall organization or biogenesis"
## [31] "acid phosphatase activity"
## [32] "intrinsic component of membrane"
## [33] "polysaccharide localization"
## [34] "response to toxic substance"
## [35] "copper ion binding"
## [36] "response to mechanical stimulus"
## [37] "transferase activity, transferring glycosyl groups"
## [38] "root system development"
## [39] "regulation of biological quality"
## [40] "cell development"
## [41] "response to antibiotic"
## [42] "phosphoric ester hydrolase activity"
## [43] "inorganic phosphate transmembrane transporter activity"
## [44] "cellular response to stress"
## [45] "phosphate ion transmembrane transporter activity"
## [46] "anchored component of membrane"
## [47] "negative regulation of cellular process"
## [48] "response to inorganic substance"
## [49] "cytoskeleton organization"
## [50] "cellular modified amino acid biosynthetic process"
## [51] "growth"
## [52] "hydrolase activity"
## [53] "regulation of meristem development"
## [54] "organophosphate ester transport"
## [55] "cellular response to stimulus"
## [56] "response to oxygen-containing compound"
## [57] "ion binding"
## [58] "small molecule metabolic process"
## [59] "response to stress"
## [60] "regulation of cell size"
## [61] "response to temperature stimulus"
## [62] "nucleobase-containing compound kinase activity"
## [63] "cytoplasm"
## [64] "organic hydroxy compound metabolic process"
## [65] "response to wounding"
## [66] "thioester metabolic process"
## [67] "protein localization to membrane"
## [68] "nucleoside bisphosphate metabolic process"
## [69] "vesicle"
## [70] "plant epidermal cell differentiation"
## [71] "response to monosaccharide"
## [72] "negative regulation of biosynthetic process"
## [73] "ER-nucleus signaling pathway"
## [74] "transporter activity"
## [75] "DNA binding"
## [76] "fluid transport"
## [77] "basic amino acid transport"
## [78] "structural constituent of cytoskeleton"
## [79] "proteasomal protein catabolic process"
## [80] "drug metabolic process"
## [81] "multidimensional cell growth"
## [82] "galactosyltransferase activity"
## [83] "nucleobase-containing small molecule metabolic process"
## [84] "organelle membrane"
## [85] "apoplast"
## [86] "root hair cell development"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.2.1.151" "3.1.4.46" "3.6.1.1" "3.4.23.12"
## [7] "2.4.1.46" "3.2.1.4" "2.4.99.18" "5.3.99.6"GO$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "Purple acid Phosphatase, N-terminal domain"
## [4] "Glycerophosphoryl diester phosphodiesterase family"
## [5] "Iron/zinc purple acid phosphatase-like protein C"
## [6] "Calcineurin-like phosphoesterase"
## [7] "Fasciclin domain"
## [8] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [9] "Calreticulin family"
## [10] "Hsp70 protein"
## [11] "PDDEXK-like family of unknown function"
## [12] "Hsp20/alpha crystallin family"
## [13] "Major Facilitator Superfamily"
## [14] "Glycosyl hydrolase family 9"
## [15] "Xylanase inhibitor C-terminal"
## [16] "Eukaryotic aspartyl protease"
## [17] "Arabinogalactan peptide"
## [18] "Thioredoxin-like domain"
## [19] "Glycosyltransferase family 28 C-terminal domain"
## [20] "Allene oxide cyclase"
## [21] "Phosphoenolpyruvate carboxylase"
## [22] "Pollen proteins Ole e I like"
## [23] "Glycosyl hydrolases family 17"
## [24] "EF-hand domain pair"
## [25] "Fantastic Four meristem regulator"
## [26] "PLAT/LH2 domain"
## [27] "UAA transporter family"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T6NPAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T6NPAZD_Low <- GO9.3 T24 DMSO
9.3.1 Induced genes
GO <- gopher(T24NPSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "methylation"
## [2] "non-membrane-bounded organelle"
## [3] "structural molecule activity"
## [4] "membrane-enclosed lumen"
## [5] "protein-containing complex"
## [6] "protein alkylation"
## [7] "cellular component organization or biogenesis"
## [8] "ribonucleoprotein complex"
## [9] "cellular nitrogen compound metabolic process"
## [10] "ribonucleoprotein complex biogenesis"
## [11] "nitrogen compound metabolic process"
## [12] "intracellular"
## [13] "DNA replication"
## [14] "organelle"
## [15] "heterocycle metabolic process"
## [16] "peptidyl-amino acid modification"
## [17] "cell population proliferation"
## [18] "pyrimidine-containing compound metabolic process"
## [19] "cell cycle"
## [20] "mitochondrial transport"
## [21] "cell division"
## [22] "macromolecule metabolic process"
## [23] "cytosol"
## [24] "cellular process"
## [25] "cellular amide metabolic process"
## [26] "nuclear transport"
## [27] "cellular aromatic compound metabolic process"
## [28] "organic cyclic compound metabolic process"
## [29] "structural constituent of ribosome"
## [30] "organelle organization"
## [31] "metabolic process"
## [32] "gene expression"
## [33] "protein localization to organelle"
## [34] "reproduction"
## [35] "chromosome organization"
## [36] "cellular response to DNA damage stimulus"
## [37] "RNA modification"
## [38] "cellular localization"
## [39] "heterocyclic compound binding"
## [40] "macromolecule localization"
## [41] "hydrolase activity, acting on acid anhydrides"
## [42] "organic cyclic compound binding"
## [43] "flower calyx development"
## [44] "post-embryonic plant morphogenesis"
## [45] "gene silencing"
## [46] "protein localization to nucleus"
## [47] "amide transport"
## [48] "ribosome"
## [49] "organelle assembly"
## [50] "peptide metabolic process"
## [51] "microtubule-based process"
## [52] "catalytic activity, acting on RNA"
## [53] "shoot system development"
## [54] "ncRNA metabolic process"
## [55] "anatomical structure formation involved in morphogenesis"
## [56] "mitochondrion organization"
## [57] "multi-organism reproductive process"
## [58] "cell cycle phase transition"
## [59] "ribonucleoprotein complex localization"
## [60] "DNA metabolic process"
## [61] "regulation of gene expression, epigenetic"
## [62] "RNA localization"
## [63] "multicellular organismal process"
## [64] "primary metabolic process"
## [65] "protein localization to mitochondrion"
## [66] "nuclease activity"
## [67] "protein-containing complex localization"
## [68] "embryo sac development"
## [69] "negative regulation of gene expression, epigenetic"
## [70] "macromolecule modification"
## [71] "developmental process"
## [72] "biosynthetic process"
## [73] "nucleobase-containing compound metabolic process"
## [74] "corolla development"
## [75] "nucleobase-containing small molecule metabolic process"
## [76] "organic substance metabolic process"
## [77] "regulation of biological process"
## [78] "chromosome segregation"
## [79] "protein import"
## [80] "response to radiation"
## [81] "gametophyte development"
## [82] "translation regulator activity"
## [83] "ribose phosphate metabolic process"
## [84] "organic substance transport"
## [85] "nitrogen compound transport"
## [86] "reproductive system development"
## [87] "multicellular organism reproduction"
## [88] "nucleotidyltransferase activity"
## [89] "regulation of reproductive process"
## [90] "catalytic activity, acting on DNA"
## [91] "nucleic acid transport"
## [92] "response to cytokinin"
## [93] "mitotic cell cycle process"
## [94] "organophosphate metabolic process"
## [95] "cellular process involved in reproduction in multicellular organism"
## [96] "nucleobase-containing compound transport"
## [97] "binding"
## [98] "regulation of cell cycle"
## [99] "kinase regulator activity"
## [100] "organophosphate biosynthetic process"
## [101] "plant organ formation"
## [102] "nucleoid"
## [103] "negative regulation of metabolic process"
## [104] "regulation of multicellular organismal process"
## [105] "mitochondrion"
## [106] "response to red or far red light"
## [107] "response to ionizing radiation"
## [108] "protein modification by small protein conjugation"
## [109] "apoplast"
## [110] "external encapsulating structure"
## [111] "histone H3-K9 modification"
## [112] "protein deubiquitination"
## [113] "symplast"
## [114] "cell junction"
## [115] "RNA binding"
## [116] "double-strand break repair"
## [117] "multicellular organism development"
## [118] "import into nucleus"
## [119] "nucleoside phosphate biosynthetic process"
## [120] "plant epidermis morphogenesis"
## [121] "post-embryonic plant organ development"
## [122] "anatomical structure homeostasis"
## [123] "isoprenoid metabolic process"
## [124] "nucleus"
## [125] "response to abiotic stimulus"
## [126] "plastid stroma"
## [127] "RNA splicing, via transesterification reactions"
## [128] "peptidyl-lysine modification"
## [129] "cellular metabolic process"
## [130] "regulation of macromolecule metabolic process"
## [131] "envelope"
## [132] "ribosomal small subunit biogenesis"
## [133] "post-embryonic development"
## [134] "organic substance biosynthetic process"
## [135] "pyruvate metabolic process"
## [136] "covalent chromatin modification"
## [137] "regulation of developmental process"
## [138] "histone kinase activity"
## [139] "cellular biosynthetic process"
## [140] "RNA processing"
## [141] "lysine metabolic process"
## [142] "single-stranded DNA binding"
## [143] "ligase activity"
## [144] "isopentenyl diphosphate metabolic process"
## [145] "protein transporter activity"
## [146] "regulation of cellular metabolic process"
## [147] "transferase activity, transferring one-carbon groups"
## [148] "chromatin organization involved in regulation of transcription"
## [149] "macromolecule transmembrane transporter activity"
## [150] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [151] "transferase activity, transferring pentosyl groups"
## [152] "response to carbohydrate"
## [153] "ribonucleoprotein complex subunit organization"
## [154] "pseudouridine synthase activity"
## [155] "genetic transfer"
## [156] "DNA replication initiation"
## [157] "DNA modification"
## [158] "RNA phosphodiester bond hydrolysis"
## [159] "chromatin silencing by small RNA"
## [160] "ribose phosphate biosynthetic process"
## [161] "transferase complex"
## [162] "DNA-dependent ATPase activity"
## [163] "anion binding"
## [164] "protein localization"
## [165] "maintenance of location"
## [166] "negative regulation of biological process"
## [167] "female gamete generation"
## [168] "nucleic acid phosphodiester bond hydrolysis"
## [169] "regulation of mitotic cell cycle"
## [170] "organelle fusion"
## [171] "response to virus"
## [172] "cellular amino acid biosynthetic process"
## [173] "regulation of shoot system development"
## [174] "intrinsic component of plasma membrane"
## [175] "regulation of DNA replication"
## [176] "thylakoid"
## [177] "cyclin-dependent protein kinase activity"
## [178] "cell fate commitment"
## [179] "stomatal complex development"
## [180] "hydrolase activity"
## [181] "isomerase activity"GO$kegg$id## [1] "3.6.4.13" "3.6.4.4" "2.7.7.6" "3.6.4.5" "3.6.4.12" "3.6.5.3"
## [7] "2.1.1.125" "1.97.1.12" "3.1.26.5" "2.4.2.14"GO$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Kinesin motor domain"
## [5] "Core histone H2A/H2B/H3/H4"
## [6] "Helicase conserved C-terminal domain"
## [7] "TCP-1/cpn60 chaperonin family"
## [8] "Cyclin, C-terminal domain"
## [9] "Pentatricopeptide repeat domain"
## [10] "60s Acidic ribosomal protein"
## [11] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [12] "DEAD/DEAH box helicase"
## [13] "Cyclin, N-terminal domain"
## [14] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [15] "Brix domain"
## [16] "Ribosomal protein L13"
## [17] "WD domain, G-beta repeat"
## [18] "MCM N-terminal domain"
## [19] "Ribosomal protein L41"
## [20] "Ribosomal protein L5"
## [21] "(Dead): PF12711"
## [22] "ribosomal L5P family C-terminus"
## [23] "3 exoribonuclease family, domain 1"
## [24] "Type III restriction enzyme, res subunit"
## [25] "Calponin homology (CH) domain"
## [26] "Elongation factor Tu GTP binding domain"
## [27] "MCM P-loop domain"
## [28] "Centromere kinetochore component CENP-T histone fold"
## [29] "Ribosomal protein L1p/L10e family"
## [30] "3 exoribonuclease family, domain 2"
## [31] "mTERF"
## [32] "Plant organelle RNA recognition domain"
## [33] "Ribosomal protein L21e"
## [34] "Tim10/DDP family zinc finger"
## [35] "Ribosomal protein L19e"
## [36] "Ribosomal S17"
## [37] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [38] "(Dead): PF06548"
## [39] "Ribosomal protein L3"
## [40] "Dip2/Utp12 Family"
## [41] "Domain of unknown function (DUF3523)"
## [42] "OB-fold nucleic acid binding domain"
## [43] "Chlorophyll A-B binding protein"
## [44] "Ribosomal protein S5, N-terminal domain"
## [45] "KOW motif"
## [46] "Ribosomal protein S5, C-terminal domain"
## [47] "Mitochondrial glycoprotein"
## [48] "NAC domain"
## [49] "Hsp20/alpha crystallin family"
## [50] "Elongation factor Tu domain 2"
## [51] "Targeting protein for Xklp2 (TPX2)"
## [52] "PPR repeat"
## [53] "Ribosomal protein S13/S18"
## [54] "KH domain"
## [55] "NOP5NT (NUC127) domain"
## [56] "Ribosomal protein S10p/S20e"
## [57] "Replication factor-A protein 1, N-terminal domain"
## [58] "Replication protein A OB domain"
## [59] "16S rRNA methyltransferase RsmB/F"
## [60] "50S ribosome-binding GTPase"
## [61] "Replication factor-A C terminal domain"
## [62] "Ribosomal protein S7e"
## [63] "40S ribosomal protein S4 C-terminus"
## [64] "Ribosomal family S4e"
## [65] "DNA-dependent RNA polymerase"
## [66] "Ribosomal protein L6, N-terminal domain"
## [67] "Ribosomal protein L6e"
## [68] "Ribosomal protein S26e"
## [69] "Nucleolar GTP-binding protein 1 (NOG1)"
## [70] "Plectin/S10 domain"
## [71] "RS4NT (NUC023) domain"
## [72] "Ribosomal protein L24e"
## [73] "Ribosomal protein L31e"
## [74] "Rad9"
## [75] "Ribosomal protein L37e"
## [76] "Ribosomal L39 protein"
## [77] "Ribosomal L28e protein family"
## [78] "DNA-directed RNA polymerase N-terminal"
## [79] "Ribosomal protein S27a"
## [80] "Ribosomal protein S8e"
## [81] "Ribosomal L22e protein family"
## [82] "Ribosomal_S17 N-terminal"
## [83] "Ribosomal protein S19e"
## [84] "Ribosomal protein L34e"
## [85] "S1 RNA binding domain"
## [86] "Ribosomal L27e protein family"
## [87] "C-terminus of histone H2A"
## [88] "Single-strand binding protein family"
## [89] "Gar1/Naf1 RNA binding region"
## [90] "Mad3/BUB1 homology region 1"
## [91] "Ribosomal protein L36e"
## [92] "Ribosomal protein S28e"
## [93] "CBF/Mak21 family"
## [94] "Ribosomal protein S30"
## [95] "GATA zinc finger"
## [96] "Elongation factor Tu C-terminal domain"
## [97] "Transcription factor S-II (TFIIS)"
## [98] "Ribosomal protein L10"
## [99] "XPG I-region"
## [100] "Toprim domain"
## [101] "Nucleosome assembly protein (NAP)"
## [102] "Zinc knuckle"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NPSDMSO_High <- GO
GO <- gopher(T24NSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "pyrimidine-containing compound metabolic process"
## [2] "ribonucleoprotein complex biogenesis"
## [3] "nuclear transport"
## [4] "protein localization to nucleus"
## [5] "ncRNA metabolic process"
## [6] "RNA modification"
## [7] "methylation"
## [8] "protein import"
## [9] "small molecule metabolic process"
## [10] "heterocycle metabolic process"
## [11] "membrane-enclosed lumen"
## [12] "RNA processing"
## [13] "transferase activity, transferring one-carbon groups"
## [14] "light-harvesting complex"
## [15] "organic cyclic compound metabolic process"
## [16] "photosynthesis"
## [17] "non-membrane-bounded organelle"
## [18] "phosphorus metabolic process"
## [19] "cellular aromatic compound metabolic process"
## [20] "protein domain specific binding"
## [21] "tetrapyrrole binding"
## [22] "copper ion binding"
## [23] "carbohydrate derivative metabolic process"
## [24] "serine family amino acid metabolic process"
## [25] "rRNA metabolic process"
## [26] "cellular nitrogen compound metabolic process"
## [27] "regulation of protein metabolic process"
## [28] "nucleobase-containing small molecule metabolic process"
## [29] "organophosphate metabolic process"
## [30] "protein localization to organelle"GO$kegg$id## [1] "1.97.1.12" "2.3.1.193" "2.7.7.27" "2.1.1.178" "2.1.1.125" "3.6.4.13"GO$pfam$name## [1] "Chlorophyll A-B binding protein"
## [2] "NOP5NT (NUC127) domain"
## [3] "Response regulator receiver domain"
## [4] "snoRNA binding domain, fibrillarin"
## [5] "PPR repeat"
## [6] "PPR repeat family"
## [7] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [8] "N-terminal domain of 16S rRNA methyltransferase RsmF"
## [9] "Helicase"
## [10] "Photosystem I reaction centre subunit VI"
## [11] "Possible tRNA binding domain"
## [12] "Noc2p family"
## [13] "Domain of unknown function (DUF1726)"
## [14] "GNAT acetyltransferase 2"
## [15] "Tim17/Tim22/Tim23/Pmp24 family"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NSDMSO_High <- GO
GO <- gopher(T24PKSDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "methylation"
## [2] "non-membrane-bounded organelle"
## [3] "structural molecule activity"
## [4] "membrane-enclosed lumen"
## [5] "protein-containing complex"
## [6] "protein alkylation"
## [7] "cellular component organization or biogenesis"
## [8] "DNA replication"
## [9] "ribonucleoprotein complex"
## [10] "ribonucleoprotein complex biogenesis"
## [11] "cellular nitrogen compound metabolic process"
## [12] "cell population proliferation"
## [13] "cell cycle"
## [14] "peptidyl-amino acid modification"
## [15] "pyrimidine-containing compound metabolic process"
## [16] "nitrogen compound metabolic process"
## [17] "organelle"
## [18] "intracellular"
## [19] "cellular amide metabolic process"
## [20] "cell division"
## [21] "cytosol"
## [22] "cellular process"
## [23] "macromolecule metabolic process"
## [24] "heterocycle metabolic process"
## [25] "organelle organization"
## [26] "mitochondrial transport"
## [27] "structural constituent of ribosome"
## [28] "nuclear transport"
## [29] "metabolic process"
## [30] "organic cyclic compound metabolic process"
## [31] "cellular aromatic compound metabolic process"
## [32] "protein localization to organelle"
## [33] "chromosome organization"
## [34] "gene expression"
## [35] "RNA modification"
## [36] "cellular response to DNA damage stimulus"
## [37] "gene silencing"
## [38] "hydrolase activity, acting on acid anhydrides"
## [39] "cellular localization"
## [40] "flower calyx development"
## [41] "ribosome"
## [42] "post-embryonic plant morphogenesis"
## [43] "cell cycle phase transition"
## [44] "reproduction"
## [45] "microtubule-based process"
## [46] "amide transport"
## [47] "organelle assembly"
## [48] "ncRNA metabolic process"
## [49] "macromolecule localization"
## [50] "shoot system development"
## [51] "peptide metabolic process"
## [52] "heterocyclic compound binding"
## [53] "DNA metabolic process"
## [54] "organic cyclic compound binding"
## [55] "anatomical structure formation involved in morphogenesis"
## [56] "macromolecule modification"
## [57] "protein localization to nucleus"
## [58] "multi-organism reproductive process"
## [59] "regulation of gene expression, epigenetic"
## [60] "catalytic activity, acting on RNA"
## [61] "nucleobase-containing small molecule metabolic process"
## [62] "nucleobase-containing compound metabolic process"
## [63] "negative regulation of gene expression, epigenetic"
## [64] "multicellular organismal process"
## [65] "corolla development"
## [66] "RNA localization"
## [67] "nucleotidyltransferase activity"
## [68] "biosynthetic process"
## [69] "ribonucleoprotein complex localization"
## [70] "regulation of biological process"
## [71] "embryo sac development"
## [72] "kinase regulator activity"
## [73] "protein localization to mitochondrion"
## [74] "nuclease activity"
## [75] "protein-containing complex localization"
## [76] "mitotic cell cycle process"
## [77] "catalytic activity, acting on DNA"
## [78] "regulation of reproductive process"
## [79] "ribose phosphate metabolic process"
## [80] "organic substance transport"
## [81] "mitochondrion organization"
## [82] "developmental process"
## [83] "gametophyte development"
## [84] "response to radiation"
## [85] "response to cytokinin"
## [86] "regulation of cell cycle"
## [87] "protein import"
## [88] "chromosome segregation"
## [89] "primary metabolic process"
## [90] "cellular process involved in reproduction in multicellular organism"
## [91] "nitrogen compound transport"
## [92] "response to ionizing radiation"
## [93] "plant organ formation"
## [94] "organophosphate metabolic process"
## [95] "organophosphate biosynthetic process"
## [96] "organic substance metabolic process"
## [97] "regulation of multicellular organismal process"
## [98] "reproductive system development"
## [99] "nucleobase-containing compound transport"
## [100] "post-embryonic plant organ development"
## [101] "multicellular organism reproduction"
## [102] "symplast"
## [103] "cell junction"
## [104] "histone H3-K9 modification"
## [105] "negative regulation of metabolic process"
## [106] "plant epidermis morphogenesis"
## [107] "nucleic acid transport"
## [108] "response to light intensity"
## [109] "translation regulator activity"
## [110] "anatomical structure homeostasis"
## [111] "nucleoid"
## [112] "protein localization"
## [113] "apoplast"
## [114] "nucleus"
## [115] "double-strand break repair"
## [116] "peptidyl-lysine modification"
## [117] "external encapsulating structure"
## [118] "import into nucleus"
## [119] "anion binding"
## [120] "ribosomal small subunit biogenesis"
## [121] "DNA replication initiation"
## [122] "response to abiotic stimulus"
## [123] "cellular biosynthetic process"
## [124] "nucleoside phosphate biosynthetic process"
## [125] "phosphorus metabolic process"
## [126] "cellular metabolic process"
## [127] "regulation of macromolecule metabolic process"
## [128] "organic substance biosynthetic process"
## [129] "histone kinase activity"
## [130] "thylakoid"
## [131] "transferase activity, transferring pentosyl groups"
## [132] "protein deubiquitination"
## [133] "binding"
## [134] "macromolecule transmembrane transporter activity"
## [135] "regulation of DNA replication"
## [136] "protein modification by small protein conjugation"
## [137] "protein transporter activity"
## [138] "isoprenoid metabolic process"
## [139] "transferase activity, transferring one-carbon groups"
## [140] "response to red or far red light"
## [141] "genetic transfer"
## [142] "hydrolase activity"
## [143] "regulation of shoot system development"
## [144] "regulation of developmental process"
## [145] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [146] "RNA processing"
## [147] "cellular response to stress"
## [148] "rRNA metabolic process"
## [149] "plastid"
## [150] "plastid stroma"
## [151] "RNA splicing, via transesterification reactions"
## [152] "multicellular organism development"
## [153] "RNA binding"
## [154] "pseudouridine synthase activity"
## [155] "cyclin-dependent protein kinase activity"
## [156] "response to virus"
## [157] "covalent chromatin modification"
## [158] "DNA-dependent ATPase activity"
## [159] "DNA modification"
## [160] "pyruvate metabolic process"
## [161] "regulation of mitotic cell cycle"
## [162] "envelope"
## [163] "serine family amino acid metabolic process"
## [164] "cytokinesis"
## [165] "negative regulation of biological process"
## [166] "RNA phosphodiester bond hydrolysis"
## [167] "regulation of cellular metabolic process"
## [168] "ribose phosphate biosynthetic process"
## [169] "organonitrogen compound metabolic process"
## [170] "post-embryonic development"
## [171] "nucleic acid phosphodiester bond hydrolysis"
## [172] "stomatal complex development"
## [173] "amide transmembrane transporter activity"
## [174] "chromatin organization involved in regulation of transcription"
## [175] "ribonucleoprotein complex subunit organization"
## [176] "response to carbohydrate"
## [177] "response to oxidative stress"
## [178] "protein serine/threonine kinase activity"
## [179] "ligase activity"
## [180] "chromatin silencing by small RNA"
## [181] "response to toxic substance"
## [182] "protein folding"
## [183] "microtubule motor activity"
## [184] "regulation of anatomical structure size"
## [185] "intrinsic component of plasma membrane"
## [186] "single-stranded RNA binding"
## [187] "cellular amino acid biosynthetic process"
## [188] "motor activity"GO$kegg$id## [1] "3.6.4.13" "3.6.4.4" "2.7.7.6" "3.6.4.12" "3.6.4.5" "1.97.1.12"
## [7] "5.99.1.3" "2.1.1.125" "3.1.26.5" "3.6.5.3" "2.4.2.14"GO$pfam$name## [1] "Kinesin motor domain"
## [2] "Cyclin, C-terminal domain"
## [3] "Core histone H2A/H2B/H3/H4"
## [4] "Cyclin, N-terminal domain"
## [5] "PPR repeat family"
## [6] "60s Acidic ribosomal protein"
## [7] "PPR repeat"
## [8] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [9] "Helicase conserved C-terminal domain"
## [10] "TCP-1/cpn60 chaperonin family"
## [11] "Brix domain"
## [12] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [13] "Chlorophyll A-B binding protein"
## [14] "MCM N-terminal domain"
## [15] "(Dead): PF12711"
## [16] "DEAD/DEAH box helicase"
## [17] "ribosomal L5P family C-terminus"
## [18] "Ribosomal protein L5"
## [19] "Calponin homology (CH) domain"
## [20] "Ribosomal protein L41"
## [21] "Ribosomal protein L1p/L10e family"
## [22] "MCM P-loop domain"
## [23] "Ribosomal protein L13"
## [24] "mTERF"
## [25] "Ribosomal protein L3"
## [26] "Domain of unknown function (DUF3523)"
## [27] "Ribosomal protein L21e"
## [28] "Elongation factor Tu GTP binding domain"
## [29] "Dip2/Utp12 Family"
## [30] "Tim10/DDP family zinc finger"
## [31] "Pentatricopeptide repeat domain"
## [32] "WD domain, G-beta repeat"
## [33] "Ribosomal S17"
## [34] "(Dead): PF06548"
## [35] "Hsp20/alpha crystallin family"
## [36] "Mitochondrial glycoprotein"
## [37] "3 exoribonuclease family, domain 1"
## [38] "KOW motif"
## [39] "Ribosomal protein S5, N-terminal domain"
## [40] "Ribosomal protein S5, C-terminal domain"
## [41] "Targeting protein for Xklp2 (TPX2)"
## [42] "Ribosomal protein S13/S18"
## [43] "NOP5NT (NUC127) domain"
## [44] "16S rRNA methyltransferase RsmB/F"
## [45] "3 exoribonuclease family, domain 2"
## [46] "Replication protein A OB domain"
## [47] "Replication factor-A protein 1, N-terminal domain"
## [48] "Replication factor-A C terminal domain"
## [49] "Ribosomal protein S10p/S20e"
## [50] "KH domain"
## [51] "OB-fold nucleic acid binding domain"
## [52] "C-terminus of histone H2A"
## [53] "Ribosomal protein S7e"
## [54] "Rad9"
## [55] "Ribosomal protein L6, N-terminal domain"
## [56] "Ribosomal protein L6e"
## [57] "Gar1/Naf1 RNA binding region"
## [58] "40S ribosomal protein S4 C-terminus"
## [59] "RS4NT (NUC023) domain"
## [60] "Ribosomal family S4e"
## [61] "Ribosomal protein L37e"
## [62] "Nucleolar GTP-binding protein 1 (NOG1)"
## [63] "Type III restriction enzyme, res subunit"
## [64] "Ribosomal_S17 N-terminal"
## [65] "Ribosomal L22e protein family"
## [66] "Ribosomal protein L34e"
## [67] "CBF/Mak21 family"
## [68] "Plectin/S10 domain"
## [69] "Ribosomal protein S27a"
## [70] "Ribosomal L27e protein family"
## [71] "Single-strand binding protein family"
## [72] "Ribosomal protein S19e"
## [73] "Elongation factor Tu domain 2"
## [74] "DNA-dependent RNA polymerase"
## [75] "DNA-directed RNA polymerase N-terminal"
## [76] "Ribosomal protein L36e"
## [77] "Ribosomal protein S30"
## [78] "Ribosomal L28e protein family"
## [79] "Ribosomal protein L24e"
## [80] "Elongation factor Tu C-terminal domain"
## [81] "Ribosomal protein S8e"
## [82] "Mad3/BUB1 homology region 1"
## [83] "Nucleosome assembly protein (NAP)"
## [84] "Ribosomal protein S17"
## [85] "Ribosomal protein L10"
## [86] "Toprim domain"
## [87] "XPG I-region"
## [88] "ATPase family associated with various cellular activities (AAA)"
## [89] "Phosphoribosyl transferase domain"
## [90] "S4 domain"
## [91] "Hsp70 protein"
## [92] "50S ribosome-binding GTPase"
## [93] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [94] "snoRNA binding domain, fibrillarin"
## [95] "Domain of unknown function (DUF4217)"
## [96] "Ribosomal protein S8"
## [97] "XPG N-terminal domain"
## [98] "Zinc-finger domain of monoamine-oxidase A repressor R1"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24PKSDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T24PKSDMSO_High <- GO
GO <- gopher(T24NPDMSO_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "non-membrane-bounded organelle"
## [2] "methylation"
## [3] "structural molecule activity"
## [4] "ribonucleoprotein complex biogenesis"
## [5] "protein-containing complex"
## [6] "ribonucleoprotein complex"
## [7] "organelle"
## [8] "cellular component organization or biogenesis"
## [9] "membrane-enclosed lumen"
## [10] "protein alkylation"
## [11] "cellular nitrogen compound metabolic process"
## [12] "intracellular"
## [13] "DNA replication"
## [14] "nitrogen compound metabolic process"
## [15] "heterocycle metabolic process"
## [16] "cell population proliferation"
## [17] "cell cycle"
## [18] "pyrimidine-containing compound metabolic process"
## [19] "peptidyl-amino acid modification"
## [20] "metabolic process"
## [21] "cellular process"
## [22] "cell division"
## [23] "macromolecule metabolic process"
## [24] "organelle organization"
## [25] "cellular aromatic compound metabolic process"
## [26] "organic cyclic compound metabolic process"
## [27] "cellular amide metabolic process"
## [28] "structural constituent of ribosome"
## [29] "thylakoid"
## [30] "ribosome"
## [31] "gene expression"
## [32] "RNA modification"
## [33] "ncRNA metabolic process"
## [34] "nuclear transport"
## [35] "gene silencing"
## [36] "mitochondrial transport"
## [37] "cell cycle phase transition"
## [38] "flower calyx development"
## [39] "organelle assembly"
## [40] "post-embryonic plant morphogenesis"
## [41] "cytosol"
## [42] "microtubule-based process"
## [43] "shoot system development"
## [44] "macromolecule modification"
## [45] "protein localization to nucleus"
## [46] "anatomical structure formation involved in morphogenesis"
## [47] "peptide metabolic process"
## [48] "protein localization to organelle"
## [49] "cellular localization"
## [50] "chromosome organization"
## [51] "cellular response to DNA damage stimulus"
## [52] "negative regulation of gene expression, epigenetic"
## [53] "mitotic cell cycle process"
## [54] "isoprenoid metabolic process"
## [55] "amide transport"
## [56] "rRNA metabolic process"
## [57] "response to cytokinin"
## [58] "corolla development"
## [59] "photosynthesis"
## [60] "hydrolase activity, acting on acid anhydrides"
## [61] "heterocyclic compound binding"
## [62] "nucleobase-containing compound metabolic process"
## [63] "reproduction"
## [64] "phosphorus metabolic process"
## [65] "biosynthetic process"
## [66] "RNA localization"
## [67] "organic cyclic compound binding"
## [68] "nucleoid"
## [69] "pyruvate metabolic process"
## [70] "plastid stroma"
## [71] "ribonucleoprotein complex localization"
## [72] "multicellular organismal process"
## [73] "macromolecule localization"
## [74] "response to red or far red light"
## [75] "protein-containing complex localization"
## [76] "regulation of cell cycle"
## [77] "serine family amino acid metabolic process"
## [78] "multi-organism reproductive process"
## [79] "regulation of gene expression, epigenetic"
## [80] "developmental process"
## [81] "primary metabolic process"
## [82] "protein localization to mitochondrion"
## [83] "kinase regulator activity"
## [84] "isopentenyl diphosphate metabolic process"
## [85] "apoplast"
## [86] "regulation of reproductive process"
## [87] "regulation of biological process"
## [88] "response to carbohydrate"
## [89] "nucleic acid transport"
## [90] "embryo sac development"
## [91] "nuclease activity"
## [92] "post-embryonic plant organ development"
## [93] "mitochondrion organization"
## [94] "multicellular organism development"
## [95] "DNA metabolic process"
## [96] "organic substance metabolic process"
## [97] "plant epidermis morphogenesis"
## [98] "protein import"
## [99] "stomatal complex development"
## [100] "envelope"
## [101] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [102] "histone H3-K9 modification"
## [103] "nucleobase-containing small molecule metabolic process"
## [104] "cellular biosynthetic process"
## [105] "organophosphate metabolic process"
## [106] "chromosome segregation"
## [107] "response to blue light"
## [108] "binding"
## [109] "response to radiation"
## [110] "organelle subcompartment"
## [111] "gametophyte development"
## [112] "nitrogen compound transport"
## [113] "organophosphate biosynthetic process"
## [114] "catalytic activity, acting on RNA"
## [115] "histone kinase activity"
## [116] "organic substance transport"
## [117] "external encapsulating structure"
## [118] "import into nucleus"
## [119] "regulation of macromolecule metabolic process"
## [120] "plastid"
## [121] "multicellular organism reproduction"
## [122] "cellular process involved in reproduction in multicellular organism"
## [123] "response to ionizing radiation"
## [124] "nucleobase-containing compound transport"
## [125] "photosystem"
## [126] "protein deubiquitination"
## [127] "protein modification by small protein conjugation"
## [128] "ribosomal small subunit biogenesis"
## [129] "regulation of mitotic cell cycle"
## [130] "symplast"
## [131] "response to red light"
## [132] "catalytic activity, acting on DNA"
## [133] "cell junction"
## [134] "cytokinesis"
## [135] "protein localization"
## [136] "regulation of DNA replication"
## [137] "NADP metabolic process"
## [138] "chromatin organization involved in regulation of transcription"
## [139] "plastid transcription"
## [140] "RNA phosphodiester bond hydrolysis"
## [141] "regulation of cellular metabolic process"
## [142] "DNA replication initiation"
## [143] "negative gravitropism"
## [144] "motor activity"
## [145] "RNA processing"
## [146] "cellular metabolic process"
## [147] "nucleotidyltransferase activity"
## [148] "plastid localization"
## [149] "transferase activity, transferring one-carbon groups"
## [150] "chromosome separation"
## [151] "ligase activity, forming nitrogen-metal bonds"
## [152] "mitochondrion"
## [153] "pseudouridine synthase activity"
## [154] "isomerase activity"
## [155] "tetrapyrrole binding"
## [156] "intrinsic component of plasma membrane"
## [157] "transferase activity, transferring pentosyl groups"
## [158] "monovalent inorganic cation transport"
## [159] "chromatin silencing by small RNA"
## [160] "tetraterpenoid metabolic process"
## [161] "organic substance biosynthetic process"GO$kegg$id## [1] "3.6.4.4" "3.6.4.13" "1.10.3.9" "1.97.1.12" "3.6.4.5" "2.7.7.6"
## [7] "5.99.1.3" "2.1.1.125" "2.1.1.43"GO$pfam$name## [1] "PPR repeat family"
## [2] "PPR repeat"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Cyclin, C-terminal domain"
## [5] "60s Acidic ribosomal protein"
## [6] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [7] "Kinesin motor domain"
## [8] "Chlorophyll A-B binding protein"
## [9] "Pentatricopeptide repeat domain"
## [10] "mTERF"
## [11] "Cyclin, N-terminal domain"
## [12] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [13] "Brix domain"
## [14] "Core histone H2A/H2B/H3/H4"
## [15] "Plant organelle RNA recognition domain"
## [16] "PPR repeat"
## [17] "Ribosomal protein L5"
## [18] "ribosomal L5P family C-terminus"
## [19] "Ribosomal protein L1p/L10e family"
## [20] "Ribosomal protein L13"
## [21] "Ribosomal protein L3"
## [22] "Dip2/Utp12 Family"
## [23] "Helicase conserved C-terminal domain"
## [24] "Ribosomal protein L21e"
## [25] "Ribosomal S17"
## [26] "(Dead): PF06548"
## [27] "Calponin homology (CH) domain"
## [28] "KOW motif"
## [29] "3 exoribonuclease family, domain 1"
## [30] "Ribosomal protein S5, N-terminal domain"
## [31] "Ribosomal protein S5, C-terminal domain"
## [32] "Targeting protein for Xklp2 (TPX2)"
## [33] "Ribosomal protein L41"
## [34] "Ribosomal protein S9/S16"
## [35] "NOP5NT (NUC127) domain"
## [36] "3 exoribonuclease family, domain 2"
## [37] "Replication factor-A protein 1, N-terminal domain"
## [38] "(Dead): PF12711"
## [39] "Ribosomal protein L6"
## [40] "Replication protein A OB domain"
## [41] "Replication factor-A C terminal domain"
## [42] "Rad9"
## [43] "Ribosomal protein S27a"
## [44] "Ribosomal protein L36e"
## [45] "PsbP"
## [46] "Ribosomal L27e protein family"
## [47] "CBF/Mak21 family"
## [48] "Plectin/S10 domain"
## [49] "Ribosomal family S4e"
## [50] "Ribosomal L22e protein family"
## [51] "RS4NT (NUC023) domain"
## [52] "40S ribosomal protein S4 C-terminus"
## [53] "Ribosomal protein L24e"
## [54] "Gar1/Naf1 RNA binding region"
## [55] "Ribosomal_S17 N-terminal"
## [56] "DNA-dependent RNA polymerase"
## [57] "DNA-directed RNA polymerase N-terminal"
## [58] "TCP-1/cpn60 chaperonin family"
## [59] "Ribosomal protein S19e"
## [60] "Ribosomal L28e protein family"
## [61] "Single-strand binding protein family"
## [62] "Ribosomal protein S8e"
## [63] "Mad3/BUB1 homology region 1"
## [64] "AP2 domain"
## [65] "Toprim domain"
## [66] "XPG I-region"
## [67] "Type III restriction enzyme, res subunit"
## [68] "DEAD/DEAH box helicase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPDMSO_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NPDMSO_High <- GO9.3.2 Repressed genes
GO <- gopher(T24NPSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "secondary metabolic process"
## [3] "benzene-containing compound metabolic process"
## [4] "liposaccharide metabolic process"
## [5] "indole-containing compound metabolic process"
## [6] "cell communication"
## [7] "cell death"
## [8] "extracellular region"
## [9] "response to external stimulus"
## [10] "localization"
## [11] "aging"
## [12] "immune system process"
## [13] "vacuole"
## [14] "protein localization to membrane"
## [15] "catabolic process"
## [16] "cell periphery"
## [17] "lipid metabolic process"
## [18] "multi-organism process"
## [19] "membrane lipid metabolic process"
## [20] "amine metabolic process"
## [21] "response to biotic stimulus"
## [22] "regulation of biological quality"
## [23] "drug metabolic process"
## [24] "catalytic activity"
## [25] "flavonoid metabolic process"
## [26] "response to wounding"
## [27] "organic hydroxy compound metabolic process"
## [28] "microbody"
## [29] "organic acid metabolic process"
## [30] "small molecule metabolic process"
## [31] "glycosyl compound metabolic process"
## [32] "response to acid chemical"
## [33] "regulation of multi-organism process"
## [34] "regulation of response to stimulus"
## [35] "endomembrane system organization"
## [36] "multi-organism cellular process"
## [37] "membrane"
## [38] "cytoplasm"
## [39] "cellular response to external stimulus"
## [40] "aromatic amino acid family metabolic process"
## [41] "protein targeting"
## [42] "response to extracellular stimulus"
## [43] "transporter activity"
## [44] "cellular modified amino acid biosynthetic process"
## [45] "small molecule biosynthetic process"
## [46] "ion transport"
## [47] "carbohydrate derivative biosynthetic process"
## [48] "aromatic compound biosynthetic process"
## [49] "cellular response to phosphate starvation"
## [50] "reactive oxygen species metabolic process"
## [51] "defense response"
## [52] "phenol-containing compound metabolic process"
## [53] "peroxisome organization"
## [54] "organic cyclic compound biosynthetic process"
## [55] "organonitrogen compound metabolic process"
## [56] "monocarboxylic acid metabolic process"
## [57] "response to stress"
## [58] "response to monosaccharide"
## [59] "protein localization to vacuole"
## [60] "oxidoreductase activity"
## [61] "plant epidermal cell differentiation"
## [62] "DNA binding"
## [63] "cellular macromolecule metabolic process"
## [64] "detoxification"
## [65] "response to nitrogen compound"
## [66] "hydrolase activity, acting on ester bonds"
## [67] "auxin metabolic process"
## [68] "heterocycle biosynthetic process"
## [69] "response to oxygen-containing compound"
## [70] "response to osmotic stress"
## [71] "sulfur compound metabolic process"
## [72] "regulation of cofactor metabolic process"
## [73] "regulation of immune system process"
## [74] "response to absence of light"
## [75] "regulation of meristem development"
## [76] "response to organic cyclic compound"
## [77] "oxygen binding"
## [78] "carbohydrate derivative catabolic process"
## [79] "polysaccharide localization"
## [80] "intracellular signal transduction"
## [81] "phosphorylation"
## [82] "cellular component macromolecule biosynthetic process"
## [83] "signal transduction by protein phosphorylation"
## [84] "glutathione transferase activity"
## [85] "nucleobase metabolic process"
## [86] "antioxidant activity"
## [87] "sulfur compound catabolic process"
## [88] "inorganic anion transport"
## [89] "ER body"
## [90] "metal ion transport"
## [91] "pollen development"
## [92] "cellular anatomical entity"
## [93] "regulation of hormone levels"
## [94] "signaling"
## [95] "dioxygenase activity"
## [96] "nucleoside diphosphate metabolic process"
## [97] "bounding membrane of organelle"
## [98] "oxidoreductase activity, acting on single donors with incorporation of molecular oxygen"
## [99] "chemical homeostasis"
## [100] "response to desiccation"
## [101] "regulation of response to stress"
## [102] "immune response"
## [103] "acid phosphatase activity"
## [104] "cell wall thickening"
## [105] "regulation of protein metabolic process"
## [106] "response to unfolded protein"
## [107] "coumarin metabolic process"
## [108] "modified amino acid binding"
## [109] "heterocycle catabolic process"
## [110] "regulation of microtubule-based process"
## [111] "response to starvation"
## [112] "structural constituent of cell wall"
## [113] "response to light stimulus"
## [114] "regulation of reactive oxygen species metabolic process"
## [115] "intramolecular oxidoreductase activity"
## [116] "phosphate ion transmembrane transporter activity"
## [117] "sulfur compound binding"
## [118] "postreplication repair"
## [119] "enzyme inhibitor activity"
## [120] "drug binding"
## [121] "cellular hormone metabolic process"
## [122] "detection of stimulus"
## [123] "cellular amine metabolic process"
## [124] "divalent inorganic cation transport"
## [125] "endoplasmic reticulum"
## [126] "stomatal movement"
## [127] "biological regulation"
## [128] "negative regulation of biosynthetic process"
## [129] "pigment catabolic process"
## [130] "cellular response to stimulus"
## [131] "organophosphate catabolic process"
## [132] "nonribosomal peptide biosynthetic process"
## [133] "response to fungus"
## [134] "external encapsulating structure organization"
## [135] "transport"
## [136] "cytoskeleton"
## [137] "protein modification process"
## [138] "peptidyl-cysteine modification"
## [139] "protein autoubiquitination"
## [140] "carbohydrate derivative metabolic process"
## [141] "nitrile metabolic process"
## [142] "IAA-amino acid conjugate hydrolase activity"
## [143] "response to karrikin"
## [144] "polysaccharide metabolic process"
## [145] "protein complex oligomerization"
## [146] "transcription factor complex"
## [147] "cofactor metabolic process"
## [148] "fluid transport"
## [149] "sucrose metabolic process"
## [150] "phosphate ion transport"
## [151] "cell development"GO$kegg$id## [1] "3.1.3.2" "2.4.1.207" "2.5.1.18" "1.11.1.9" "1.11.1.7" "1.2.4.4"
## [7] "3.6.3.27" "5.3.99.6"GO$pfam$name## [1] "non-haem dioxygenase in morphine synthesis N-terminal"
## [2] "Purple acid Phosphatase, N-terminal domain"
## [3] "2OG-Fe(II) oxygenase superfamily"
## [4] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [5] "Glycosyl hydrolases family 16"
## [6] "Iron/zinc purple acid phosphatase-like protein C"
## [7] "Jacalin-like lectin domain"
## [8] "Cytochrome P450"
## [9] "Major Facilitator Superfamily"
## [10] "Glutathione S-transferase, N-terminal domain"
## [11] "Scorpion toxin-like domain"
## [12] "AMP-binding enzyme"
## [13] "Papain family cysteine protease"
## [14] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [15] "Phosphoesterase family"
## [16] "FMN-dependent dehydrogenase"
## [17] "Gamma-glutamyl cyclotransferase, AIG2-like"
## [18] "POT family"
## [19] "PLAT/LH2 domain"
## [20] "Calcineurin-like phosphoesterase"
## [21] "Allene oxide cyclase"
## [22] "Alcohol dehydrogenase GroES-like domain"
## [23] "SPX domain"
## [24] "Lipase (class 3)"
## [25] "Sugar (and other) transporter"
## [26] "Glycerophosphoryl diester phosphodiesterase family"
## [27] "Yippee zinc-binding/DNA-binding /Mis18, centromere assembly"
## [28] "Phosphatidylinositol-specific phospholipase C, X domain"
## [29] "Sucrose synthase"
## [30] "Glycosyl hydrolase family 1"
## [31] "Glutathione S-transferase, C-terminal domain"
## [32] "Peroxidase"
## [33] "Major intrinsic protein"
## [34] "AMP-binding enzyme C-terminal domain"
## [35] "AhpC/TSA family"
## [36] "Cathepsin propeptide inhibitor domain (I29)"
## [37] "Protein of unknown function, DUF538"
## [38] "Universal stress protein family"
## [39] "Saposin-like type B, region 1"
## [40] "Saposin-like type B, region 2"
## [41] "MatE"
## [42] "NAD binding domain of 6-phosphogluconate dehydrogenase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NPSDMSO_Low <- GO
GO <- gopher(T24NSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "immune system process"
## [3] "response to chemical"
## [4] "respiratory burst"
## [5] "protein localization to membrane"
## [6] "cell communication"
## [7] "cell death"
## [8] "indole-containing compound metabolic process"
## [9] "benzene-containing compound metabolic process"
## [10] "multi-organism process"
## [11] "response to nitrogen compound"
## [12] "secondary metabolic process"
## [13] "extracellular region"
## [14] "external encapsulating structure"
## [15] "signaling"
## [16] "response to light intensity"
## [17] "transcription regulator activity"
## [18] "response to drug"
## [19] "regulation of biological quality"
## [20] "response to endogenous stimulus"
## [21] "response to oxygen-containing compound"
## [22] "organic acid metabolic process"
## [23] "biological regulation"
## [24] "DNA binding"
## [25] "drug metabolic process"
## [26] "hydrolase activity, acting on glycosyl bonds"
## [27] "glycosyl compound metabolic process"
## [28] "amine metabolic process"
## [29] "response to biotic stimulus"
## [30] "aging"
## [31] "protein folding"
## [32] "protein targeting"
## [33] "organic hydroxy compound metabolic process"
## [34] "defense response"
## [35] "multi-organism cellular process"
## [36] "regulation of multi-organism process"
## [37] "localization"
## [38] "reactive oxygen species metabolic process"
## [39] "aromatic compound biosynthetic process"
## [40] "response to heat"
## [41] "oxidoreductase activity"
## [42] "response to wounding"
## [43] "phenol-containing compound metabolic process"
## [44] "small molecule biosynthetic process"
## [45] "vacuole"
## [46] "structural constituent of cell wall"
## [47] "organic cyclic compound biosynthetic process"
## [48] "regulation of response to stimulus"
## [49] "response to oxidative stress"
## [50] "external encapsulating structure organization"
## [51] "response to external stimulus"
## [52] "response to monosaccharide"
## [53] "heterocycle biosynthetic process"
## [54] "RNA metabolic process"
## [55] "cell periphery"
## [56] "monocarboxylic acid metabolic process"
## [57] "regulation of cofactor metabolic process"
## [58] "shade avoidance"
## [59] "olefin metabolic process"
## [60] "flavonoid metabolic process"
## [61] "response to unfolded protein"
## [62] "aromatic amino acid family metabolic process"
## [63] "anaerobic respiration"
## [64] "oxygen binding"
## [65] "intracellular signal transduction"
## [66] "ion transport"
## [67] "inorganic anion transport"
## [68] "de-etiolation"
## [69] "response to antibiotic"
## [70] "transferase activity, transferring glycosyl groups"
## [71] "organonitrogen compound catabolic process"
## [72] "phytoalexin metabolic process"
## [73] "heat acclimation"
## [74] "cation binding"
## [75] "phosphorylation"
## [76] "glucosyltransferase activity"
## [77] "carboxylic ester hydrolase activity"
## [78] "antioxidant activity"
## [79] "response to insect"
## [80] "plant-type cell wall"
## [81] "NAD(P)H dehydrogenase complex (plastoquinone)"
## [82] "monocarboxylic acid biosynthetic process"
## [83] "signal transduction by protein phosphorylation"GO$kegg$id## [1] "2.4.1.207" "3.2.1.21" "1.11.1.7"GO$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "AP2 domain"
## [4] "Hsp20/alpha crystallin family"
## [5] "Transport and Golgi organisation 2"
## [6] "zinc-finger of the FCS-type, C2-C2"
## [7] "Cytochrome P450"
## [8] "Peroxidase"
## [9] "POT family"
## [10] "Glycosyl hydrolase family 1"
## [11] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [12] "Jacalin-like lectin domain"
## [13] "Purine nucleobase transmembrane transport"
## [14] "Phosphate-induced protein 1 conserved region"
## [15] "Dormancy/auxin associated protein"
## [16] "CP12 domain"
## [17] "Glycosyl hydrolase family 3 N terminal domain"
## [18] "Dehydrin"
## [19] "Glycosyl hydrolase family 3 C-terminal domain"
## [20] "No apical meristem (NAM) protein"
## [21] "HD-ZIP protein N terminus"
## [22] "WRKY DNA -binding domain"
## [23] "Domain of unknown function (DUF4228)"
## [24] "Aluminium induced protein"
## [25] "Cold acclimation protein WCOR413"
## [26] "Domain of unknown function (DUF4666)"
## [27] "Wound-induced protein WI12"
## [28] "Domain associated at C-terminal with AAA"
## [29] "Homeobox associated leucine zipper"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NSDMSO_Low <- GO
GO <- gopher(T24PKSDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "cell communication"
## [3] "secondary metabolic process"
## [4] "extracellular region"
## [5] "indole-containing compound metabolic process"
## [6] "liposaccharide metabolic process"
## [7] "response to external stimulus"
## [8] "benzene-containing compound metabolic process"
## [9] "amine metabolic process"
## [10] "cell periphery"
## [11] "cell death"
## [12] "protein localization to membrane"
## [13] "membrane lipid metabolic process"
## [14] "multi-organism process"
## [15] "lipid metabolic process"
## [16] "immune system process"
## [17] "regulation of biological quality"
## [18] "aging"
## [19] "response to wounding"
## [20] "response to biotic stimulus"
## [21] "flavonoid metabolic process"
## [22] "vacuole"
## [23] "drug metabolic process"
## [24] "localization"
## [25] "glycosyl compound metabolic process"
## [26] "organic acid metabolic process"
## [27] "transporter activity"
## [28] "response to acid chemical"
## [29] "catabolic process"
## [30] "endomembrane system organization"
## [31] "ion transport"
## [32] "cellular response to external stimulus"
## [33] "carbohydrate derivative biosynthetic process"
## [34] "small molecule metabolic process"
## [35] "small molecule biosynthetic process"
## [36] "response to extracellular stimulus"
## [37] "aromatic amino acid family metabolic process"
## [38] "cellular modified amino acid biosynthetic process"
## [39] "organic hydroxy compound metabolic process"
## [40] "protein targeting"
## [41] "catalytic activity"
## [42] "reactive oxygen species metabolic process"
## [43] "structural constituent of cell wall"
## [44] "membrane"
## [45] "response to oxygen-containing compound"
## [46] "cellular response to phosphate starvation"
## [47] "regulation of response to stimulus"
## [48] "aromatic compound biosynthetic process"
## [49] "hydrolase activity, acting on ester bonds"
## [50] "defense response"
## [51] "regulation of multi-organism process"
## [52] "phenol-containing compound metabolic process"
## [53] "multi-organism cellular process"
## [54] "sulfur compound metabolic process"
## [55] "oxygen binding"
## [56] "detoxification"
## [57] "response to nitrogen compound"
## [58] "DNA binding"
## [59] "heterocycle biosynthetic process"
## [60] "phosphorylation"
## [61] "response to absence of light"
## [62] "organic cyclic compound biosynthetic process"
## [63] "auxin metabolic process"
## [64] "biological regulation"
## [65] "external encapsulating structure organization"
## [66] "monocarboxylic acid metabolic process"
## [67] "response to osmotic stress"
## [68] "acid phosphatase activity"
## [69] "signaling"
## [70] "intracellular signal transduction"
## [71] "nucleoside diphosphate metabolic process"
## [72] "microbody"
## [73] "peroxisome organization"
## [74] "response to monosaccharide"
## [75] "response to organic cyclic compound"
## [76] "heterocycle catabolic process"
## [77] "oxidoreductase activity, acting on single donors with incorporation of molecular oxygen"
## [78] "negative regulation of biosynthetic process"
## [79] "sulfur compound biosynthetic process"
## [80] "phosphate ion transmembrane transporter activity"
## [81] "cellular macromolecule metabolic process"
## [82] "regulation of microtubule-based process"
## [83] "oligopeptide transport"
## [84] "postreplication repair"
## [85] "antioxidant activity"
## [86] "drug binding"
## [87] "cellular response to stimulus"
## [88] "response to light stimulus"
## [89] "polysaccharide localization"
## [90] "pollen development"
## [91] "olefin metabolic process"
## [92] "metal ion transport"
## [93] "cellular hormone metabolic process"
## [94] "response to unfolded protein"
## [95] "signal transduction by protein phosphorylation"
## [96] "de-etiolation"
## [97] "dioxygenase activity"
## [98] "respiratory burst"
## [99] "pigment catabolic process"
## [100] "fluid transport"
## [101] "UDP-glycosyltransferase activity"
## [102] "response to karrikin"
## [103] "regulation of hormone levels"
## [104] "chemical homeostasis"
## [105] "regulation of carbohydrate metabolic process"
## [106] "ER body"
## [107] "regulation of cofactor metabolic process"
## [108] "organonitrogen compound metabolic process"
## [109] "protein autoubiquitination"
## [110] "ligand-gated channel activity"
## [111] "polysaccharide metabolic process"
## [112] "peptidase regulator activity"
## [113] "regulation of immune system process"
## [114] "divalent inorganic cation transport"
## [115] "bounding membrane of organelle"
## [116] "cyclic nucleotide binding"
## [117] "lipid binding"
## [118] "response to stress"
## [119] "transferase activity, transferring glycosyl groups"
## [120] "urea transmembrane transporter activity"
## [121] "cellular amine metabolic process"
## [122] "peptidyl-cysteine modification"
## [123] "response to fungus"
## [124] "coumarin metabolic process"
## [125] "external encapsulating structure"
## [126] "regulation of meristem development"
## [127] "aromatic compound catabolic process"
## [128] "organic cyclic compound catabolic process"
## [129] "response to starvation"
## [130] "response to desiccation"
## [131] "alkaloid metabolic process"
## [132] "phloem or xylem histogenesis"
## [133] "cytoplasm"
## [134] "sulfur compound binding"
## [135] "inorganic anion transport"
## [136] "sucrose metabolic process"
## [137] "response to cold"
## [138] "nucleobase metabolic process"
## [139] "modified amino acid binding"
## [140] "regulation of primary metabolic process"
## [141] "carbohydrate derivative catabolic process"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "5.3.99.6" "3.1.4.11" "3.6.3.27" "1.11.1.7"GO$pfam$name## [1] "Purple acid Phosphatase, N-terminal domain"
## [2] "Glycosyl hydrolases family 16"
## [3] "Iron/zinc purple acid phosphatase-like protein C"
## [4] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [5] "Major Facilitator Superfamily"
## [6] "Cytochrome P450"
## [7] "Jacalin-like lectin domain"
## [8] "Lipase (class 3)"
## [9] "non-haem dioxygenase in morphine synthesis N-terminal"
## [10] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [11] "Calcineurin-like phosphoesterase"
## [12] "AMP-binding enzyme"
## [13] "2OG-Fe(II) oxygenase superfamily"
## [14] "Universal stress protein family"
## [15] "MatE"
## [16] "Eukaryotic aspartyl protease"
## [17] "PLAT/LH2 domain"
## [18] "Sugar (and other) transporter"
## [19] "Glutathione S-transferase, N-terminal domain"
## [20] "Allene oxide cyclase"
## [21] "Glycerophosphoryl diester phosphodiesterase family"
## [22] "Phosphatidylinositol-specific phospholipase C, X domain"
## [23] "Proteolipid membrane potential modulator"
## [24] "Scorpion toxin-like domain"
## [25] "Glycosyl hydrolase family 1"
## [26] "Ethylene-responsive binding factor-associated repression"
## [27] "Purine nucleobase transmembrane transport"
## [28] "TIR domain"
## [29] "POT family"
## [30] "AMP-binding enzyme C-terminal domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24PKSDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24PKSDMSO_Low <- GO
GO <- gopher(T24NPDMSO_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "secondary metabolic process"
## [3] "cell communication"
## [4] "liposaccharide metabolic process"
## [5] "indole-containing compound metabolic process"
## [6] "extracellular region"
## [7] "benzene-containing compound metabolic process"
## [8] "membrane lipid metabolic process"
## [9] "response to external stimulus"
## [10] "protein localization to membrane"
## [11] "cell periphery"
## [12] "cell death"
## [13] "immune system process"
## [14] "amine metabolic process"
## [15] "multi-organism process"
## [16] "flavonoid metabolic process"
## [17] "aging"
## [18] "drug metabolic process"
## [19] "localization"
## [20] "glycosyl compound metabolic process"
## [21] "response to wounding"
## [22] "response to biotic stimulus"
## [23] "carbohydrate derivative biosynthetic process"
## [24] "regulation of biological quality"
## [25] "transporter activity"
## [26] "lipid metabolic process"
## [27] "vacuole"
## [28] "cellular response to external stimulus"
## [29] "ion transport"
## [30] "organic hydroxy compound metabolic process"
## [31] "response to acid chemical"
## [32] "small molecule biosynthetic process"
## [33] "cellular response to phosphate starvation"
## [34] "response to extracellular stimulus"
## [35] "aromatic compound biosynthetic process"
## [36] "regulation of multi-organism process"
## [37] "membrane"
## [38] "organic acid metabolic process"
## [39] "phosphorylation"
## [40] "biological regulation"
## [41] "endomembrane system organization"
## [42] "chemical homeostasis"
## [43] "organic cyclic compound biosynthetic process"
## [44] "catalytic activity"
## [45] "signaling"
## [46] "response to nitrogen compound"
## [47] "DNA binding"
## [48] "phenol-containing compound metabolic process"
## [49] "heterocycle biosynthetic process"
## [50] "protein targeting"
## [51] "response to stress"
## [52] "response to unfolded protein"
## [53] "cellular modified amino acid biosynthetic process"
## [54] "multi-organism cellular process"
## [55] "reactive oxygen species metabolic process"
## [56] "aromatic amino acid family metabolic process"
## [57] "sulfur compound metabolic process"
## [58] "protein localization to vacuole"
## [59] "cellular component macromolecule biosynthetic process"
## [60] "cellular macromolecule metabolic process"
## [61] "structural constituent of cell wall"
## [62] "cellular response to stimulus"
## [63] "response to oxygen-containing compound"
## [64] "small molecule metabolic process"
## [65] "regulation of response to stimulus"
## [66] "response to organic cyclic compound"
## [67] "pollen development"
## [68] "external encapsulating structure organization"
## [69] "oxygen binding"
## [70] "response to osmotic stress"
## [71] "hydrolase activity, acting on ester bonds"
## [72] "polysaccharide localization"
## [73] "regulation of meristem development"
## [74] "negative regulation of biosynthetic process"
## [75] "regulation of immune system process"
## [76] "regulation of microtubule-based process"
## [77] "regulation of cofactor metabolic process"
## [78] "carbohydrate derivative catabolic process"
## [79] "modified amino acid binding"
## [80] "catabolic process"
## [81] "defense response"
## [82] "phloem or xylem histogenesis"
## [83] "sulfur compound binding"
## [84] "nucleobase metabolic process"
## [85] "cell development"
## [86] "glutathione transferase activity"
## [87] "antioxidant activity"
## [88] "regulation of hormone levels"
## [89] "response to karrikin"
## [90] "stomatal movement"
## [91] "phosphate ion transmembrane transporter activity"
## [92] "cellular anatomical entity"
## [93] "polysaccharide metabolic process"
## [94] "monocarboxylic acid metabolic process"
## [95] "acid phosphatase activity"
## [96] "microbody"
## [97] "inorganic anion transport"
## [98] "oxidoreductase activity"
## [99] "dioxygenase activity"
## [100] "transcription factor complex"
## [101] "auxin metabolic process"
## [102] "sulfur compound catabolic process"
## [103] "response to drug"
## [104] "amide binding"
## [105] "adenylyltransferase activity"
## [106] "sulfur compound biosynthetic process"
## [107] "inorganic phosphate transmembrane transporter activity"
## [108] "regulation of cell size"
## [109] "nucleoside diphosphate metabolic process"
## [110] "UDP-glycosyltransferase activity"
## [111] "plant epidermal cell differentiation"
## [112] "phosphoric ester hydrolase activity"
## [113] "detection of stimulus"
## [114] "regulation of seedling development"
## [115] "cellular hormone metabolic process"
## [116] "endoplasmic reticulum"
## [117] "ER-nucleus signaling pathway"
## [118] "respiratory burst"
## [119] "protein modification process"
## [120] "immune response"
## [121] "response to starvation"GO$kegg$id## [1] "2.4.1.207" "1.11.1.7" "3.1.3.2" "2.5.1.18" "3.1.4.11"GO$pfam$name## [1] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [2] "Glycosyl hydrolases family 16"
## [3] "Purple acid Phosphatase, N-terminal domain"
## [4] "Jacalin-like lectin domain"
## [5] "Iron/zinc purple acid phosphatase-like protein C"
## [6] "non-haem dioxygenase in morphine synthesis N-terminal"
## [7] "Lipase (class 3)"
## [8] "2OG-Fe(II) oxygenase superfamily"
## [9] "Scorpion toxin-like domain"
## [10] "Glutathione S-transferase, N-terminal domain"
## [11] "POT family"
## [12] "Universal stress protein family"
## [13] "Cytochrome P450"
## [14] "Peroxidase"
## [15] "PLAT/LH2 domain"
## [16] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [17] "Purine nucleobase transmembrane transport"
## [18] "Major Facilitator Superfamily"
## [19] "MatE"
## [20] "Glycerophosphoryl diester phosphodiesterase family"
## [21] "Phosphatidylinositol-specific phospholipase C, X domain"
## [22] "Calcineurin-like phosphoesterase"
## [23] "Glutathione S-transferase, C-terminal domain"
## [24] "Major intrinsic protein"
## [25] "ZIP Zinc transporter"
## [26] "Domain associated at C-terminal with AAA"
## [27] "Gamma-glutamyl cyclotransferase, AIG2-like"
## [28] "Phosphatidylinositol-specific phospholipase C, Y domain"
## [29] "AMP-binding enzyme"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPDMSO_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NPDMSO_Low <- GO9.4 T24 AZD
9.4.1 Induced genes
GO <- gopher(T24NPSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "small nucleolar ribonucleoprotein complex"
## [2] "mitochondrion"
## [3] "transcription regulator activity"
## [4] "RNA modification"
## [5] "ribonucleoprotein complex biogenesis"
## [6] "pyrimidine-containing compound metabolic process"
## [7] "response to karrikin"
## [8] "protein localization to nucleus"
## [9] "nuclear transport"
## [10] "response to oxygen-containing compound"
## [11] "oligosaccharide metabolic process"
## [12] "oligopeptide transport"
## [13] "regulation of primary metabolic process"
## [14] "response to acid chemical"
## [15] "starch metabolic process"
## [16] "mitochondrial RNA metabolic process"
## [17] "heterocycle metabolic process"
## [18] "heterocycle biosynthetic process"
## [19] "light-harvesting complex"
## [20] "transferase activity"
## [21] "cellular aromatic compound metabolic process"
## [22] "flavonoid metabolic process"
## [23] "aromatic compound biosynthetic process"
## [24] "fatty acid derivative metabolic process"
## [25] "organic cyclic compound biosynthetic process"
## [26] "very long-chain fatty acid metabolic process"
## [27] "anion transport"
## [28] "nitrogen compound transport"
## [29] "transferase activity, transferring one-carbon groups"
## [30] "cuticle development"
## [31] "DNA binding"
## [32] "post-embryonic plant morphogenesis"
## [33] "ncRNA metabolic process"GO$kegg$id## [1] "2.3.1.199" "3.6.4.13" "2.4.2.51" "1.2.1.13"GO$pfam$name## [1] "PPR repeat family"
## [2] "PPR repeat"
## [3] "PPR repeat"
## [4] "DYW family of nucleic acid deaminases"
## [5] "Pentatricopeptide repeat domain"
## [6] "mTERF"
## [7] "Chlorophyll A-B binding protein"
## [8] "Dimerisation domain"
## [9] "O-methyltransferase domain"
## [10] "FAE1/Type III polyketide synthase-like protein"
## [11] "3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal"
## [12] "Cytochrome P450"
## [13] "AP2 domain"
## [14] "Glutamine synthetase, beta-Grasp domain"
## [15] "Response regulator receiver domain"
## [16] "Plant organelle RNA recognition domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NPSAZD_High <- GO
GO <- gopher(T24NSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to karrikin"
## [2] "secondary metabolic process"
## [3] "oligopeptide transport"
## [4] "flavonoid metabolic process"
## [5] "response to acid chemical"
## [6] "aromatic compound biosynthetic process"
## [7] "ion transport"
## [8] "heterocycle biosynthetic process"
## [9] "response to oxygen-containing compound"
## [10] "light-harvesting complex"
## [11] "organic cyclic compound biosynthetic process"
## [12] "anion transport"
## [13] "protein localization to nucleus"
## [14] "nuclear transport"
## [15] "starch metabolic process"
## [16] "organic acid transport"
## [17] "pyrimidine-containing compound metabolic process"
## [18] "single-stranded RNA binding"
## [19] "DNA binding"
## [20] "fatty acid derivative metabolic process"
## [21] "regulation of primary metabolic process"
## [22] "oligosaccharide metabolic process"
## [23] "plastid organization"
## [24] "transcription regulator activity"
## [25] "cellular component disassembly"GO$kegg$id## [1] "1.3.1.74" "2.7.7.59" "1.3.1.27" "6.3.1.2" "6.2.1.34" "6.2.1.12" "3.1.1.1"GO$pfam$name## [1] "Zinc-binding dehydrogenase"
## [2] "Cytochrome P450"
## [3] "Dimerisation domain"
## [4] "non-haem dioxygenase in morphine synthesis N-terminal"
## [5] "O-methyltransferase domain"
## [6] "N-terminal domain of oxidoreductase"
## [7] "2OG-Fe(II) oxygenase superfamily"
## [8] "Alpha amylase, catalytic domain"
## [9] "Chlorophyll A-B binding protein"
## [10] "3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal"
## [11] "Response regulator receiver domain"
## [12] "Glutamine synthetase, catalytic domain"
## [13] "AMP-binding enzyme"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NSAZD_High <- GO
GO <- gopher(T24PKSAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "transcription regulator activity"
## [2] "response to karrikin"
## [3] "ribonucleoprotein complex biogenesis"
## [4] "small nucleolar ribonucleoprotein complex"
## [5] "light-harvesting complex"
## [6] "oligopeptide transport"
## [7] "protein localization to nucleus"
## [8] "plastid organization"
## [9] "nuclear transport"
## [10] "pyrimidine-containing compound metabolic process"
## [11] "flavonoid metabolic process"
## [12] "secondary metabolic process"
## [13] "DNA binding"
## [14] "heterocycle biosynthetic process"
## [15] "aromatic compound biosynthetic process"
## [16] "oligosaccharide metabolic process"
## [17] "ion transport"
## [18] "regulation of primary metabolic process"
## [19] "organic cyclic compound biosynthetic process"
## [20] "response to disaccharide"
## [21] "response to oxygen-containing compound"
## [22] "fatty acid derivative metabolic process"
## [23] "starch metabolic process"
## [24] "photosynthesis"
## [25] "RNA metabolic process"
## [26] "oxygen binding"GO$kegg$id## [1] "3.1.1.1" "2.4.2.51" "1.2.1.13"GO$pfam$name## [1] "Chlorophyll A-B binding protein"
## [2] "Dimerisation domain"
## [3] "Cytochrome P450"
## [4] "O-methyltransferase domain"
## [5] "Response regulator receiver domain"
## [6] "Late embryogenesis abundant protein"
## [7] "Carboxylesterase family"
## [8] "Myb-like DNA-binding domain"
## [9] "Glutamine synthetase, beta-Grasp domain"
## [10] "Zinc-binding dehydrogenase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24PKSAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T24PKSAZD_High <- GO
GO <- gopher(T24NPAZD_High,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "thylakoid"
## [2] "plastid organization"
## [3] "photosynthesis"
## [4] "organelle subcompartment"
## [5] "NADP metabolic process"
## [6] "generation of precursor metabolites and energy"
## [7] "glucose 6-phosphate metabolic process"
## [8] "ion transport"
## [9] "plastid"
## [10] "tetrapyrrole metabolic process"
## [11] "secondary metabolic process"
## [12] "ribonucleoprotein complex biogenesis"
## [13] "ncRNA metabolic process"
## [14] "membrane organization"
## [15] "pigment metabolic process"
## [16] "response to blue light"
## [17] "light-harvesting complex"
## [18] "response to red light"
## [19] "establishment of localization in cell"
## [20] "response to far red light"
## [21] "protein-containing complex subunit organization"
## [22] "regulation of protein metabolic process"
## [23] "oxidation-reduction process"
## [24] "aging"
## [25] "response to stimulus"
## [26] "protein localization to membrane"
## [27] "PSII associated light-harvesting complex II catabolic process"
## [28] "oligosaccharide metabolic process"
## [29] "shoot system morphogenesis"
## [30] "organic acid metabolic process"
## [31] "starch metabolic process"
## [32] "organelle localization"
## [33] "cofactor metabolic process"
## [34] "oxygen binding"
## [35] "response to oxygen-containing compound"
## [36] "tetrapyrrole binding"
## [37] "sulfur compound metabolic process"
## [38] "plastid stroma"
## [39] "plastid transcription"
## [40] "plastid envelope"
## [41] "protein localization to chloroplast"
## [42] "lipid metabolic process"
## [43] "biological regulation"
## [44] "RNA metabolic process"
## [45] "response to disaccharide"
## [46] "cellular component biogenesis"
## [47] "transcription regulator activity"
## [48] "serine family amino acid metabolic process"
## [49] "plastoglobule"
## [50] "response to acid chemical"
## [51] "leaf development"
## [52] "DNA binding"
## [53] "cellular aldehyde metabolic process"
## [54] "nucleoid"
## [55] "envelope"
## [56] "dephosphorylation"
## [57] "localization"
## [58] "single-stranded RNA binding"
## [59] "plastid localization"
## [60] "rRNA metabolic process"
## [61] "drug metabolic process"
## [62] "small molecule biosynthetic process"
## [63] "isoprenoid metabolic process"
## [64] "defense response"
## [65] "cellular homeostasis"
## [66] "oxidoreductase activity"
## [67] "organic acid transport"
## [68] "Group II intron splicing"
## [69] "positive regulation of metabolic process"
## [70] "flavonoid metabolic process"
## [71] "cellular response to environmental stimulus"
## [72] "glycosyl compound metabolic process"
## [73] "carbon fixation"
## [74] "oligopeptide transport"
## [75] "multi-organism cellular process"
## [76] "membrane-bounded organelle"
## [77] "cell death"
## [78] "small molecule metabolic process"
## [79] "nucleic acid metabolic process"
## [80] "protein targeting"
## [81] "unsaturated fatty acid metabolic process"
## [82] "response to karrikin"
## [83] "cytoplasmic chromosome"
## [84] "isopentenyl diphosphate metabolic process"
## [85] "chemical homeostasis"
## [86] "transmembrane transport"
## [87] "response to wounding"
## [88] "methyl jasmonate esterase activity"
## [89] "immune system process"
## [90] "rhythmic process"
## [91] "positive regulation of molecular function"
## [92] "small nucleolar ribonucleoprotein complex"
## [93] "molecular transducer activity"
## [94] "regulation of seedling development"
## [95] "regulation of localization"
## [96] "regulation of molecular function"
## [97] "regulation of primary metabolic process"
## [98] "ER body"
## [99] "proton transmembrane transport"
## [100] "cellular response to sucrose starvation"
## [101] "alanine-glyoxylate transaminase activity"
## [102] "negative regulation of developmental process"
## [103] "protein repair"
## [104] "benzene-containing compound metabolic process"
## [105] "cytoplasm"
## [106] "organic cyclic compound biosynthetic process"
## [107] "cellular component assembly"
## [108] "multicellular organism development"
## [109] "secondary active transmembrane transporter activity"
## [110] "stomatal complex development"
## [111] "endoplasmic reticulum"
## [112] "response to organic substance"
## [113] "nitrogen cycle metabolic process"
## [114] "peptidyl-cysteine modification"
## [115] "reactive nitrogen species metabolic process"
## [116] "response to carbohydrate"
## [117] "photosynthetic electron transport in photosystem I"
## [118] "photosynthesis, light reaction"
## [119] "microbody"
## [120] "response to light stimulus"
## [121] "response to endogenous stimulus"
## [122] "cofactor binding"
## [123] "protein modification process"
## [124] "reactive oxygen species metabolic process"
## [125] "response to chemical"
## [126] "organic hydroxy compound metabolic process"
## [127] "pigment catabolic process"
## [128] "methyl salicylate esterase activity"
## [129] "methyl indole-3-acetate esterase activity"
## [130] "photosystem"
## [131] "regulation of seed development"
## [132] "negative regulation of multicellular organismal process"
## [133] "oxylipin metabolic process"GO$kegg$id## [1] "1.10.3.9" "1.97.1.12" "3.2.1.21" "2.6.1.44" "1.2.4.4"
## [6] "3.1.1.1" "6.3.1.2" "1.14.13.173"GO$pfam$name## [1] "Chlorophyll A-B binding protein"
## [2] "Cytochrome P450"
## [3] "NB-ARC domain"
## [4] "Glutamine synthetase, beta-Grasp domain"
## [5] "non-haem dioxygenase in morphine synthesis N-terminal"
## [6] "Glycosyl hydrolase family 1"
## [7] "AP2 domain"
## [8] "CCT motif"
## [9] "Zinc-binding dehydrogenase"
## [10] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [11] "CP12 domain"
## [12] "Glutamine synthetase, catalytic domain"
## [13] "Dimerisation domain"
## [14] "Major Facilitator Superfamily"
## [15] "O-methyltransferase domain"
## [16] "B-box zinc finger"
## [17] "2OG-Fe(II) oxygenase superfamily"
## [18] "VQ motif"
## [19] "PsbP"
## [20] "Aminotransferase class-III"
## [21] "Alcohol dehydrogenase GroES-like domain"
## [22] "Carboxylesterase family"
## [23] "Response regulator receiver domain"
## [24] "Acyl-CoA dehydrogenase, N-terminal domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPAZD_High.txt", sep = "\t",
row.names = FALSE)
GO_T24NPAZD_High <- GO9.4.2 Repressed genes
GO <- gopher(T24NPSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "response to stimulus"
## [2] "extracellular region"
## [3] "cell communication"
## [4] "cell periphery"
## [5] "response to light intensity"
## [6] "liposaccharide metabolic process"
## [7] "response to drug"
## [8] "membrane lipid metabolic process"
## [9] "immune system process"
## [10] "external encapsulating structure"
## [11] "response to nitrogen compound"
## [12] "protein localization to membrane"
## [13] "response to external stimulus"
## [14] "membrane"
## [15] "response to heat"
## [16] "regulation of biological quality"
## [17] "multi-organism process"
## [18] "protein folding"
## [19] "response to oxygen-containing compound"
## [20] "lipid metabolic process"
## [21] "vacuole"
## [22] "acid phosphatase activity"
## [23] "indole-containing compound metabolic process"
## [24] "benzene-containing compound metabolic process"
## [25] "respiratory burst"
## [26] "DNA binding"
## [27] "response to oxidative stress"
## [28] "response to monosaccharide"
## [29] "cell death"
## [30] "cellular response to external stimulus"
## [31] "olefin metabolic process"
## [32] "cellular response to stimulus"
## [33] "regulation of meristem development"
## [34] "signaling"
## [35] "response to antibiotic"
## [36] "cellular response to phosphate starvation"
## [37] "inorganic anion transport"
## [38] "response to wounding"
## [39] "organic hydroxy compound metabolic process"
## [40] "response to extracellular stimulus"
## [41] "response to chemical"
## [42] "symplast"
## [43] "drug metabolic process"
## [44] "cell junction"
## [45] "polysaccharide localization"
## [46] "modified amino acid binding"
## [47] "biological regulation"
## [48] "antioxidant activity"
## [49] "phosphate ion transmembrane transporter activity"
## [50] "secondary metabolic process"
## [51] "sulfur compound binding"
## [52] "response to stress"
## [53] "transporter activity"
## [54] "aromatic compound biosynthetic process"
## [55] "response to biotic stimulus"
## [56] "hydrolase activity, acting on glycosyl bonds"
## [57] "cellular macromolecule metabolic process"
## [58] "aging"
## [59] "oxidoreductase activity, acting on peroxide as acceptor"
## [60] "localization"
## [61] "reactive oxygen species metabolic process"
## [62] "response to toxic substance"
## [63] "protein targeting"
## [64] "phosphorylation"
## [65] "monocarboxylic acid metabolic process"
## [66] "heterocycle biosynthetic process"
## [67] "meristem maintenance"
## [68] "amine metabolic process"
## [69] "shade avoidance"
## [70] "chemical homeostasis"
## [71] "organic acid metabolic process"
## [72] "small molecule metabolic process"
## [73] "proteasomal protein catabolic process"
## [74] "syncytium formation"
## [75] "endoplasmic reticulum"
## [76] "ion transport"
## [77] "intramolecular oxidoreductase activity"
## [78] "defense response, incompatible interaction"
## [79] "regulation of cofactor metabolic process"
## [80] "amide binding"
## [81] "regulation of cell size"
## [82] "NAD(P)H dehydrogenase complex (plastoquinone)"
## [83] "oligosaccharide biosynthetic process"
## [84] "response to endogenous stimulus"
## [85] "regulation of nuclear division"
## [86] "anchored component of membrane"
## [87] "phosphoric ester hydrolase activity"
## [88] "intracellular signal transduction"
## [89] "ion binding"
## [90] "ER-nucleus signaling pathway"
## [91] "phosphate ion transport"
## [92] "plant-type cell wall"
## [93] "cellular anatomical entity"
## [94] "carbohydrate derivative metabolic process"
## [95] "metal ion transport"
## [96] "negative regulation of biosynthetic process"
## [97] "glutathione transferase activity"
## [98] "response to mechanical stimulus"
## [99] "response to endoplasmic reticulum stress"
## [100] "hydrolase activity"GO$kegg$id## [1] "3.1.3.2" "1.11.1.7" "5.3.4.1" "2.4.1.207" "3.4.23.12" "1.10.3.3"
## [7] "3.6.1.1" "3.1.3.12" "1.11.1.9" "2.4.1.46" "5.1.3.2"GO$pfam$name## [1] "Purple acid Phosphatase, N-terminal domain"
## [2] "Hsp20/alpha crystallin family"
## [3] "Iron/zinc purple acid phosphatase-like protein C"
## [4] "Calcineurin-like phosphoesterase"
## [5] "AP2 domain"
## [6] "Major Facilitator Superfamily"
## [7] "PDDEXK-like family of unknown function"
## [8] "Core histone H2A/H2B/H3/H4"
## [9] "Centromere kinetochore component CENP-T histone fold"
## [10] "Peroxidase"
## [11] "Glutathione S-transferase, C-terminal domain"
## [12] "Cotton fibre expressed protein"
## [13] "Glycosyl hydrolases family 16"
## [14] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [15] "Thioredoxin-like domain"
## [16] "Tyrosine phosphatase family"
## [17] "EF-hand domain pair"
## [18] "Calreticulin family"
## [19] "PLAT/LH2 domain"
## [20] "Glycerophosphoryl diester phosphodiesterase family"
## [21] "Multicopper oxidase"
## [22] "Multicopper oxidase"
## [23] "Major intrinsic protein"
## [24] "C2H2-type zinc finger"
## [25] "Protein of unknown function (DUF642)"
## [26] "HAD superfamily, subfamily IIIB (Acid phosphatase)"
## [27] "Glutathione S-transferase, N-terminal domain"
## [28] "No apical meristem (NAM) protein"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NPSAZD_Low <- GO
GO <- gopher(T24NSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "extracellular region"
## [2] "external encapsulating structure"
## [3] "cell periphery"
## [4] "response to stimulus"
## [5] "DNA replication"
## [6] "protein localization to membrane"
## [7] "protein folding"
## [8] "response to light intensity"
## [9] "DNA binding"
## [10] "cell communication"
## [11] "membrane"
## [12] "immune system process"
## [13] "anchored component of membrane"
## [14] "regulation of meristem development"
## [15] "response to heat"
## [16] "vacuole"
## [17] "response to drug"
## [18] "benzene-containing compound metabolic process"
## [19] "symplast"
## [20] "cell junction"
## [21] "membrane lipid metabolic process"
## [22] "acid phosphatase activity"
## [23] "response to oxidative stress"
## [24] "cell wall organization or biogenesis"
## [25] "indole-containing compound metabolic process"
## [26] "cellular response to stimulus"
## [27] "response to external stimulus"
## [28] "intrinsic component of membrane"
## [29] "chromosome"
## [30] "response to oxygen-containing compound"
## [31] "regulation of biological quality"
## [32] "cellular macromolecule metabolic process"
## [33] "cell population proliferation"
## [34] "growth"
## [35] "biological regulation"
## [36] "response to chemical"
## [37] "regulation of cell cycle"
## [38] "multi-organism process"
## [39] "hydrolase activity, acting on glycosyl bonds"
## [40] "response to monosaccharide"
## [41] "oxidoreductase activity, acting on peroxide as acceptor"
## [42] "response to red light"
## [43] "response to nitrogen compound"
## [44] "cell death"
## [45] "response to antibiotic"
## [46] "antioxidant activity"
## [47] "organic hydroxy compound metabolic process"
## [48] "de-etiolation"
## [49] "phosphorylation"
## [50] "response to far red light"
## [51] "meristem maintenance"
## [52] "hydrolase activity"
## [53] "plant-type cell wall"
## [54] "lipid metabolic process"
## [55] "transferase activity, transferring glycosyl groups"
## [56] "molecular function regulator"
## [57] "liposaccharide metabolic process"
## [58] "protein targeting"
## [59] "carbohydrate metabolic process"
## [60] "drug metabolic process"
## [61] "regulation of response to stress"
## [62] "respiratory burst"
## [63] "DNA geometric change"
## [64] "divalent inorganic cation transport"
## [65] "response to stress"
## [66] "modified amino acid binding"
## [67] "protein-DNA complex"
## [68] "water transmembrane transporter activity"
## [69] "amine metabolic process"
## [70] "fluid transport"
## [71] "regulation of cell size"
## [72] "copper ion binding"
## [73] "DNA replication initiation"
## [74] "regulation of multi-organism process"GO$kegg$id## [1] "3.1.3.2" "2.4.1.207" "3.4.23.12" "1.11.1.7" "4.2.2.2" "5.3.4.1"
## [7] "1.10.3.3" "2.4.1.46"GO$pfam$name## [1] "Core histone H2A/H2B/H3/H4"
## [2] "Centromere kinetochore component CENP-T histone fold"
## [3] "Glycosyl hydrolases family 16"
## [4] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [5] "MCM N-terminal domain"
## [6] "MCM P-loop domain"
## [7] "Hsp70 protein"
## [8] "Iron/zinc purple acid phosphatase-like protein C"
## [9] "Purple acid Phosphatase, N-terminal domain"
## [10] "Hsp20/alpha crystallin family"
## [11] "Cotton fibre expressed protein"
## [12] "PDDEXK-like family of unknown function"
## [13] "Late embryogenesis abundant protein"
## [14] "Major intrinsic protein"
## [15] "Peroxidase"
## [16] "Pectate lyase"
## [17] "AP2 domain"
## [18] "Multicopper oxidase"
## [19] "Calreticulin family"
## [20] "Calcineurin-like phosphoesterase"
## [21] "Multicopper oxidase"
## [22] "Glycerophosphoryl diester phosphodiesterase family"
## [23] "Leucine Rich Repeat"
## [24] "Sec61beta family"
## [25] "Aluminium induced protein"
## [26] "HAD superfamily, subfamily IIIB (Acid phosphatase)"
## [27] "Protein of unknown function (DUF642)"
## [28] "Multicopper oxidase"
## [29] "Eukaryotic aspartyl protease"
## [30] "Glycosyl hydrolases family 32 C terminal"
## [31] "Leucine rich repeat N-terminal domain"
## [32] "Glycosyl hydrolases family 32 N-terminal domain"
## [33] "Profilin"
## [34] "zinc-finger of the FCS-type, C2-C2"
## [35] "Pectinacetylesterase"
## [36] "Allene oxide cyclase"
## [37] "Arabinogalactan peptide"
## [38] "Glycosyl hydrolases family 17"
## [39] "Glycosyltransferase family 28 C-terminal domain"
## [40] "Transport and Golgi organisation 2"
## [41] "Phosphate-induced protein 1 conserved region"
## [42] "Thioredoxin-like domain"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NSAZD_Low <- GO
GO <- gopher(T24PKSAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "extracellular region"
## [2] "cell periphery"
## [3] "response to stimulus"
## [4] "cell communication"
## [5] "membrane lipid metabolic process"
## [6] "liposaccharide metabolic process"
## [7] "external encapsulating structure"
## [8] "membrane"
## [9] "protein localization to membrane"
## [10] "response to external stimulus"
## [11] "lipid metabolic process"
## [12] "cellular response to external stimulus"
## [13] "symplast"
## [14] "cell junction"
## [15] "regulation of biological quality"
## [16] "indole-containing compound metabolic process"
## [17] "immune system process"
## [18] "response to extracellular stimulus"
## [19] "response to nitrogen compound"
## [20] "cellular response to phosphate starvation"
## [21] "vacuole"
## [22] "transporter activity"
## [23] "phosphate ion transmembrane transporter activity"
## [24] "cellular response to stimulus"
## [25] "DNA binding"
## [26] "cell death"
## [27] "regulation of meristem development"
## [28] "localization"
## [29] "hydrolase activity, acting on glycosyl bonds"
## [30] "benzene-containing compound metabolic process"
## [31] "response to light intensity"
## [32] "inorganic anion transport"
## [33] "plant-type cell wall"
## [34] "amine metabolic process"
## [35] "regulation of multi-organism process"
## [36] "multi-organism process"
## [37] "respiratory burst"
## [38] "acid phosphatase activity"
## [39] "antioxidant activity"
## [40] "response to oxygen-containing compound"
## [41] "phosphate ion transport"
## [42] "cell wall organization or biogenesis"
## [43] "response to monosaccharide"
## [44] "response to drug"
## [45] "syncytium formation"
## [46] "oligosaccharide biosynthetic process"
## [47] "endomembrane system"
## [48] "organic hydroxy compound metabolic process"
## [49] "external encapsulating structure organization"
## [50] "oxidoreductase activity, acting on peroxide as acceptor"
## [51] "NAD(P)H dehydrogenase complex (plastoquinone)"
## [52] "phosphorylation"
## [53] "carbohydrate derivative metabolic process"
## [54] "drug metabolic process"
## [55] "cellular macromolecule metabolic process"
## [56] "hydrolase activity"
## [57] "polysaccharide localization"
## [58] "transferase activity, transferring glycosyl groups"
## [59] "negative regulation of biosynthetic process"
## [60] "aromatic compound biosynthetic process"
## [61] "anchored component of membrane"
## [62] "meristem maintenance"
## [63] "intramolecular oxidoreductase activity"
## [64] "growth"
## [65] "modified amino acid binding"
## [66] "trehalose metabolic process"
## [67] "carbohydrate metabolic process"
## [68] "tissue development"
## [69] "cellular response to stress"
## [70] "intrinsic component of membrane"
## [71] "root system development"
## [72] "cellular modified amino acid biosynthetic process"
## [73] "signaling"
## [74] "heterocycle biosynthetic process"
## [75] "copper ion binding"
## [76] "ER-nucleus signaling pathway"
## [77] "biological regulation"
## [78] "secondary metabolic process"
## [79] "response to oxidative stress"
## [80] "sulfur compound binding"
## [81] "plant epidermal cell differentiation"
## [82] "protein targeting"
## [83] "defense response, incompatible interaction"GO$kegg$id## [1] "3.1.3.2" "1.11.1.7" "3.1.3.12" "3.4.23.12" "5.3.4.1" "2.4.1.207"
## [7] "3.6.1.1" "1.10.3.3" "2.4.1.46"GO$pfam$name## [1] "Purple acid Phosphatase, N-terminal domain"
## [2] "Iron/zinc purple acid phosphatase-like protein C"
## [3] "Peroxidase"
## [4] "Cotton fibre expressed protein"
## [5] "Major Facilitator Superfamily"
## [6] "Glycosyl hydrolases family 16"
## [7] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [8] "Calcineurin-like phosphoesterase"
## [9] "Protein of unknown function (DUF642)"
## [10] "SPX domain"
## [11] "Thioredoxin-like domain"
## [12] "Late embryogenesis abundant protein"
## [13] "Multicopper oxidase"
## [14] "Multicopper oxidase"
## [15] "Calreticulin family"
## [16] "Glycerophosphoryl diester phosphodiesterase family"
## [17] "PLAT/LH2 domain"
## [18] "Multicopper oxidase"
## [19] "Trehalose-phosphatase"
## [20] "AUX/IAA family"
## [21] "Glutathione S-transferase, C-terminal domain"
## [22] "Pectate lyase"
## [23] "ZIP Zinc transporter"
## [24] "Pectinacetylesterase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24PKSAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24PKSAZD_Low <- GO
GO <- gopher(T24NPAZD_Low,background=rownames(vsd)[rowSums(vsd)>0],url="athaliana")## No enrichments found in task: mapmanGO$go$name## [1] "cell periphery"
## [2] "extracellular region"
## [3] "endomembrane system"
## [4] "membrane"
## [5] "cell wall organization or biogenesis"
## [6] "liposaccharide metabolic process"
## [7] "membrane lipid metabolic process"
## [8] "external encapsulating structure"
## [9] "symplast"
## [10] "cell junction"
## [11] "carbohydrate metabolic process"
## [12] "external encapsulating structure organization"
## [13] "growth"
## [14] "cellular response to phosphate starvation"
## [15] "response to stimulus"
## [16] "regulation of meristem development"
## [17] "root system development"
## [18] "copper ion binding"
## [19] "DNA binding"
## [20] "protein localization to membrane"
## [21] "cell communication"
## [22] "response to heat"
## [23] "hydrolase activity, acting on glycosyl bonds"
## [24] "vacuole"
## [25] "phosphate ion transport"
## [26] "intrinsic component of membrane"
## [27] "meristem maintenance"
## [28] "tissue development"
## [29] "response to light intensity"
## [30] "DNA replication"
## [31] "cell development"
## [32] "vesicle"
## [33] "response to external stimulus"
## [34] "polysaccharide localization"
## [35] "regulation of cell size"
## [36] "plant epidermal cell differentiation"
## [37] "pigmentation"
## [38] "anchored component of membrane"
## [39] "syncytium formation"
## [40] "response to drug"
## [41] "protein folding"
## [42] "regulation of biological quality"
## [43] "acid phosphatase activity"
## [44] "cellular response to external stimulus"
## [45] "cellular macromolecule metabolic process"
## [46] "galacturonan metabolic process"
## [47] "cellular metabolic compound salvage"
## [48] "phosphorylation"
## [49] "cytoskeleton organization"
## [50] "phosphoric ester hydrolase activity"
## [51] "root hair cell development"
## [52] "multidimensional cell growth"
## [53] "purine-containing compound metabolic process"
## [54] "response to endoplasmic reticulum stress"
## [55] "oligosaccharide biosynthetic process"
## [56] "nucleobase-containing compound kinase activity"
## [57] "transferase activity, transferring glycosyl groups"
## [58] "response to extracellular stimulus"
## [59] "cellular modified amino acid biosynthetic process"
## [60] "cellular response to stimulus"
## [61] "phosphate ion transmembrane transporter activity"
## [62] "nucleotide-sugar metabolic process"
## [63] "oxidoreductase complex"
## [64] "phloem or xylem histogenesis"
## [65] "apoplast"
## [66] "meristem growth"
## [67] "ribose phosphate metabolic process"
## [68] "regulation of cell cycle"
## [69] "response to mechanical stimulus"
## [70] "carbohydrate derivative binding"
## [71] "regulation of developmental process"
## [72] "sulfur compound metabolic process"
## [73] "regulation of growth"
## [74] "trehalose metabolic process"
## [75] "response to wounding"
## [76] "organonitrogen compound metabolic process"
## [77] "carbohydrate derivative metabolic process"
## [78] "nucleobase-containing small molecule metabolic process"
## [79] "small molecule metabolic process"
## [80] "embryo sac central cell differentiation"
## [81] "lipid metabolic process"
## [82] "response to oxidative stress"
## [83] "proteasomal protein catabolic process"
## [84] "chemical homeostasis"
## [85] "developmental growth"
## [86] "mitochondrial envelope"
## [87] "inorganic phosphate transmembrane transporter activity"
## [88] "cellular response to stress"
## [89] "nucleoside phosphate binding"
## [90] "regulation of response to stress"
## [91] "divalent inorganic cation transport"
## [92] "cell population proliferation"
## [93] "response to desiccation"
## [94] "tubulin complex"
## [95] "response to cyclopentenone"
## [96] "response to nitrogen compound"
## [97] "cellular component morphogenesis"
## [98] "purine nucleotide binding"
## [99] "phosphotransferase activity, phosphate group as acceptor"
## [100] "amine metabolic process"GO$kegg$id## [1] "2.4.1.207" "3.1.3.2" "3.2.1.4" "1.11.1.7" "3.2.1.39"GO$pfam$name## [1] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [2] "Glycosyl hydrolases family 16"
## [3] "Fasciclin domain"
## [4] "Glycosyl hydrolase family 9"
## [5] "Purple acid Phosphatase, N-terminal domain"
## [6] "Glycerophosphoryl diester phosphodiesterase family"
## [7] "MCM N-terminal domain"
## [8] "MCM P-loop domain"
## [9] "Thioredoxin-like domain"
## [10] "Iron/zinc purple acid phosphatase-like protein C"
## [11] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [12] "Lytic transglycolase"
## [13] "Arabinogalactan peptide"
## [14] "Calcineurin-like phosphoesterase"
## [15] "Protein of unknown function (DUF642)"
## [16] "Eukaryotic aspartyl protease"
## [17] "Profilin"
## [18] "Glycosyl transferase family 8"
## [19] "Pollen allergen"
## [20] "Hsp20/alpha crystallin family"
## [21] "Calreticulin family"
## [22] "Cotton fibre expressed protein"
## [23] "Glycosyl hydrolases family 17"
## [24] "Leucine rich repeat N-terminal domain"
## [25] "Multicopper oxidase"
## [26] "Tubulin C-terminal domain"
## [27] "Multicopper oxidase"
## [28] "Multicopper oxidase"
## [29] "Protein of unknown function (DUF1635)"
## [30] "Peroxidase"
## [31] "Hsp70 protein"
## [32] "Pollen proteins Ole e I like"
## [33] "X8 domain"
## [34] "Core histone H2A/H2B/H3/H4"
## [35] "Tubulin/FtsZ family, GTPase domain"
## [36] "Trehalose-phosphatase"write.table(data.frame(GO$go$id, GO$go$padj), file = "GO_T24NPAZD_Low.txt", sep = "\t",
row.names = FALSE)
GO_T24NPAZD_Low <- GO10 Session Info
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] jsonlite_1.6 vsn_3.54.0
## [3] VennDiagram_1.6.20 futile.logger_1.4.3
## [5] tximport_1.14.0 forcats_0.4.0
## [7] stringr_1.4.0 dplyr_0.8.3
## [9] purrr_0.3.3 readr_1.3.1
## [11] tidyr_1.0.0 tibble_2.1.3
## [13] tidyverse_1.3.0 scatterplot3d_0.3-41
## [15] RColorBrewer_1.1-2 plotly_4.9.1
## [17] pander_0.6.3 magrittr_1.5
## [19] LSD_4.0-0 limma_3.42.0
## [21] hyperSpec_0.99-20180627 ggplot2_3.2.1
## [23] lattice_0.20-38 here_0.1
## [25] gplots_3.0.1.1 DESeq2_1.26.0
## [27] SummarizedExperiment_1.16.0 DelayedArray_0.12.0
## [29] BiocParallel_1.20.0 matrixStats_0.55.0
## [31] Biobase_2.46.0 GenomicRanges_1.38.0
## [33] GenomeInfoDb_1.22.0 IRanges_2.20.1
## [35] S4Vectors_0.24.0 BiocGenerics_0.32.0
## [37] data.table_1.12.6
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 rprojroot_1.3-2 htmlTable_1.13.2
## [4] XVector_0.26.0 fs_1.3.1 base64enc_0.1-3
## [7] rstudioapi_0.10 affyio_1.56.0 bit64_0.9-7
## [10] AnnotationDbi_1.48.0 lubridate_1.7.4 xml2_1.2.2
## [13] splines_3.6.1 geneplotter_1.64.0 knitr_1.26
## [16] zeallot_0.1.0 Formula_1.2-3 broom_0.5.2
## [19] annotate_1.64.0 cluster_2.1.0 dbplyr_1.4.2
## [22] BiocManager_1.30.10 compiler_3.6.1 httr_1.4.1
## [25] backports_1.1.5 assertthat_0.2.1 Matrix_1.2-18
## [28] lazyeval_0.2.2 cli_1.1.0 formatR_1.7
## [31] acepack_1.4.1 htmltools_0.4.0 tools_3.6.1
## [34] affy_1.64.0 gtable_0.3.0 glue_1.3.1
## [37] GenomeInfoDbData_1.2.2 Rcpp_1.0.3 cellranger_1.1.0
## [40] vctrs_0.2.0 preprocessCore_1.48.0 gdata_2.18.0
## [43] nlme_3.1-142 xfun_0.11 rvest_0.3.5
## [46] testthat_2.3.0 lifecycle_0.1.0 gtools_3.8.1
## [49] XML_3.98-1.20 zlibbioc_1.32.0 scales_1.1.0
## [52] hms_0.5.2 lambda.r_1.2.4 curl_4.2
## [55] yaml_2.2.0 memoise_1.1.0 gridExtra_2.3
## [58] rpart_4.1-15 latticeExtra_0.6-28 stringi_1.4.3
## [61] RSQLite_2.1.2 highr_0.8 genefilter_1.68.0
## [64] checkmate_1.9.4 caTools_1.17.1.2 rlang_0.4.2
## [67] pkgconfig_2.0.3 bitops_1.0-6 evaluate_0.14
## [70] htmlwidgets_1.5.1 bit_1.1-14 tidyselect_0.2.5
## [73] R6_2.4.1 generics_0.0.2 Hmisc_4.3-0
## [76] DBI_1.0.0 pillar_1.4.2 haven_2.2.0
## [79] foreign_0.8-72 withr_2.1.2 survival_3.1-7
## [82] RCurl_1.95-4.12 nnet_7.3-12 modelr_0.1.5
## [85] crayon_1.3.4 futile.options_1.0.1 KernSmooth_2.23-16
## [88] rmarkdown_1.18 locfit_1.5-9.1 readxl_1.3.1
## [91] blob_1.2.0 reprex_0.3.0 digest_0.6.23
## [94] xtable_1.8-4 munsell_0.5.0 viridisLite_0.3.0